Five-step scale from benign to pathogenic. This variant is likely pathogenic. Select a step to read what it means.
This variantScenario
BenignPathogenic
Likely pathogenic.A likely pathogenic classification under the recorded framework.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
About MSH2
MSH2 is a tumor suppressor gene that encodes a key protein in the DNA mismatch repair system, which finds and fixes errors made during DNA replication. The MSH2 protein pairs with MSH6 or MSH3 to form complexes that recognize mismatched base pairs and trigger their repair. Inherited mutations in MSH2 cause Lynch syndrome (hereditary nonpolyposis colorectal cancer), predisposing to colorectal, endometrial, ovarian, and other cancers, and biallelic mutations cause constitutional mismatch repair deficiency. Loss of MSH2 function increases the mutation rate and drives tumor development, particularly in colorectal and endometrial cancers, and mismatch-repair-deficient tumors respond particularly well to immune checkpoint inhibitor therapies.
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Criteria may be applied incorrectly, sources may be misread, and a
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Double-check every criterion and its underlying evidence
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01The reasoning
How it was classified
The recorded framework is ClinGen MSH2 VCEP v2.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Met (Strong): canonical +1 splice-donor variant predicted to skip in-frame exon 12 (SpliceAI delta 1.00), deleting a functionally critical ~82-amino-acid region. Not upgraded to Very Strong because no RNA assay confirmed the splice defect.
PM2Supporting
PM2 · supporting
Met (Supporting): absent from gnomAD v4.1 (AF = 0), below the <1-in-50,000 (<0.00002) allele-frequency threshold.
PP4Supporting
PP4 · supporting
Met (Supporting): one MSI-H colorectal tumor in a documented carrier (PMID:16142001, 6-marker panel) satisfies the VCEP PP4_Supporting rule.
PP5Supporting
PP5 · supporting
Met (Supporting): ClinVar 3-star InSiGHT expert panel classifies this variant Likely pathogenic.
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Likely pathogenic
Likely Pathogenic under the InSiGHT MSH2 VCEP v2.0: PVS1 strong (canonical +1 donor, in-frame exon 12 skipping) plus PM2, PP4, PP5 supporting satisfies Rule 12 (1 Strong + >=2 Supporting), with no conflicting benign evidence.
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1
gnomAD v2.1
Population frequency
Not recorded
gnomAD v4.1 allele counts were not recorded for this variant.
ACMG/AMP criteria under ClinGen MSH2 VCEP v2.0, with the data and sources behind each one.
28 criteria with recorded statuses: 4 met · 5 not met · 8 not assessed · 11 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH2 Version 2.0 (cspec doc 1577628936, precedence rank 1); generic ACMG/AMP used only as fallback, which was not needed.
Consequence: c.2005+1G>A is a canonical +1 donor splice variant of MSH2 intron 12 (exon 12 donor). SpliceAI predicts complete donor loss (DS_DL 1.0) with a secondary cryptic donor gain at intron 12 +30 (DS_DG 0.74); both predicted outcomes are in-frame (exon 12 skipping deletes 246 nt = 82 codons; +30 cryptic donor retains 30 nt = 10 codons), so no frameshift and no NMD is expected.
PVS1 met at Strong: exon 12 (c.1760-c.2005, 246 nt) is in-frame and its encoded region (residues ~587-669) is functionally critical - it contains the EXO1-interaction region (601-671) and the ATP-binding Walker A motif (669-676, Lys675) per UniProt P43246 - satisfying the VCEP rule for IVS+/-1/+/-2 variants with in-frame skipping of a critical region (PVS1_Strong). PVS1 Very Strong is not met (no frameshift/NMD; no mRNA assay confirmation).
PM4 and BP3 are both officially Not Applicable under the InSiGHT MSH2 VCEP v2.0; the variant is additionally not an in-frame indel (PM4) nor an in-frame indel in a repeat region (BP3).
No downloaded full-text publication reports the exact allele c.2005+1G>A (checked all 7 full texts; PMID:15849733 lists only c.2005+1G>T and c.2005+2T>C at the same intron 12 donor, classified as splice defects), so no publication is cited as variant-specific evidence for this group.
Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH2 Version 2.0 (cspec doc 1577628936), framework_mode = vcep, precedence_rank 1. An applicable gene-specific specification exists, so generic ACMG/AMP was not substituted for any criterion in this group.
Variant class: NM_000251.3:c.2005+1G>A is a canonical +1 splice-donor variant (intron 12, exon boundary 12i; NP_000242.1:p.?; SpliceAI max delta 1.00, DS_DL 1.0, DS_DG 0.74). It is not a missense substitution and carries no amino-acid change, which drives the inapplicability of all residue/domain-level criteria in this group.
PM1, PP2, and BP1 are declared 'Not applicable' by the MSH2 VCEP itself (no recognized mutational hotspots for PM1; missense-based rationale not used for PP2; BP1 not used because the VCEP does not apply missense-in-LOF-gene reasoning). Status: not_applicable for each.
PS1 and PM5 are formally 'Applicable' in the CSPEC but their rules are structurally limited to missense substitutions (same amino-acid change for PS1; different missense change at the same residue for PM5) and, for PS1 only, to variants at the same NON-canonical splice nucleotide as a confirmed P/LP splice variant. A canonical +1 splice-donor variant satisfies none of these conditions, so both are not_applicable for this variant class; this is consistent with the pm5_candidates recommendation level (not_applicable, eligible_for_classic_pm5_search = false).
No criterion in this group is met. No same-residue missense comparator and no same-nucleotide splice comparator exist in the collected evidence bundle, and none of the seven downloaded full texts mention c.2005+1G>A or any c.2005+1 variant (targeted grep for '2005+1' returned no hits); the collected literature was triaged to other criteria (PP3/PP4/PP5/PS4/BS3 domains) and was not used here.
ClinVar final classifications (Pathogenic x3 clinical laboratories, Likely pathogenic x1 clinical laboratory, InSiGHT expert panel Likely pathogenic) were noted for context only and were NOT used to infer any criterion in this group, per citation-grounding rules.
Framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH2 v2.0 (cspec, framework_mode=vcep); generic ACMG/AMP not used because an applicable VCEP specification exists.
No proband, parental-testing, de novo, segregation, or non-segregation evidence exists for NM_000251.3:c.2005+1G>A in any case-bundle artifact (review_manifest, case_summary, prefetch, evidence, literature_pass, vcep_materials, source_registry, fulltext_map) or in the available full texts.
PS2 not_assessed: de novo points cannot be computed because no de novo occurrence or parental confirmation is reported for any carrier.
PM6 not_applicable: the InSiGHT MSH2 VCEP v2.0 declares PM6 not applicable; assumed de novo evidence is scored within the PS2 points system.
PP1 not_assessed: no segregation data; combined Bayes LR cannot be computed.
BS4 not_assessed: no non-segregation data; combined Bayes LR cannot be computed.
The only variant-position literature hit (PMID:15849733, c.2005+1G>T and c.2005+2T>C) concerns different nucleotide changes at the same splice donor and carries no segregation/de novo detail; it cannot substitute for evidence on the exact variant.
PS3 and BS3 were adjudicated under the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification for MSH2 v2.0 (cspec), which applies in this case (framework_mode=vcep); generic ACMG PS3/BS3 were not used.
Both PS3 and BS3 require variant-specific functional evidence (calibrated assay functional odds, flowchart-based MMR function assessment, or mRNA/allelic-expression analyses). No such data exist for NM_000251.3(MSH2):c.2005+1G>A in the case bundle or in the reviewed full texts, so both criteria are returned as not_assessed with the specific data gaps identified.
PMID:16142001 documents the exact variant (MSH2 IVS12+1 G>A) as a case observation (MSI-H tumor, IHC not performed, Amsterdam-positive family) — tumor phenotype evidence relevant to PP4, not a functional assay, and insufficient for PS3 or BS3.
PMID:15849733 reports c.2005+1G>T and c.2005+2T>C at the same splice donor nucleotide with r.? (RNA not assessed); these are different alleles and must not be conflated with c.2005+1G>A, and neither provides functional assay data.
PMID:24362816 confirms that canonical splice-site substitutions in the InSiGHT database were predominantly classified as Class 4 because of the lack of functional RNA analyses, consistent with the absence of PS3/BS3-level data for this variant.
The VCEP-calibrated MMR assay catalog (SVI documentation xlsx) and the functional assay flowchart were reviewed as the PS3/BS3 application framework; no variant-specific result for c.2005+1G>A is present in any of the nine validated assays.
Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification for MSH2 v2.0 (CSPEC doc 1577628936, precedence rank 1). PS4 is explicitly Not Applicable; PP4 and BP5 are Applicable; PP5/BP6 are marked Not Applicable by the VCEP but PP5 is applied at supporting via the global exact-variant ClinVar 3-star expert-panel rule.
PP4 met (Supporting): PMID:16142001 documents the exact variant (MSH2 IVS12+1 G>A = c.2005+1G>A) in a patient with an MSI-H colorectal tumor (6-marker panel: BAT25, BAT26, BAT40, LmycVpA, D16S512, D16S515; MSI-H = >=2 unstable markers), IHC not performed, Amsterdam criteria met. One MSI-H CRC tumor = PP4 Supporting under the VCEP rule.
PS4 not applicable: VCEP explicitly disallows PS4 for MMR variant classification (proband counting replaced by tumor IHC under PP4); no case-control enrichment data for this variant exists in the bundle.
PP5 met (Supporting): ClinVar VCV000090835 contains an exact-variant expert-panel classification - InSiGHT, Likely pathogenic, reviewed by expert panel (3 stars), germline, Lynch syndrome (SCV000107361, 2019-06-21).
BP5 not assessed: no MSS / retained-MMR-IHC / inconsistent-MMR-loss tumor data and no BRAF V600E or MLH1 methylation data for carriers of this variant; the only tumor datum available (MSI-H) runs opposite to BP5.
BP6 not met: no benign/likely-benign expert-panel classification exists for this exact variant; the sole expert-panel classification is Likely pathogenic (pathogenic direction).
The allelic evidence group contributes no scored evidence to the classification: PM3 could not be assessed because the bundle contains no biallelic/compound-heterozygous observation of c.2005+1G>A with a second P/LP MSH2 variant in a CMMRD-consistent patient, and no phase/zygosity information for any observation.
BP2 is not applicable under the governing InSiGHT MSH2 VCEP v2.0 specification, which explicitly replaces it with BS2 (and uses PM3 for biallelic CMMRD evidence); BP2 therefore contributes no benign evidence.
Absence of allelic evidence does not count against pathogenicity: the variant is a canonical splice donor variant (c.2005+1G>A) whose biallelic (CMMRD) phenotype would only be expected in rare compound-heterozygous cases, and the lack of such records in this bundle is an evidence gap, not a benign observation.
No literature source in the bundle contains the exact variant; PMID 15849733 reports only the different allele c.2005+1G>T at the same nucleotide, which must not be conflated with the queried variant.
PP3: not_applicable. c.2005+1G>A is a canonical +1 splice-donor variant; the VCEP PP3 splice sub-rule covers only non-canonical splicing nucleotides (SpliceAI delta >= 0.2, Walker et al 2023), and the VCEP PVS1 rule explicitly forbids combining PVS1 with PP3 for canonical IVS+/-1,2 variants. The missense in-silico path (HCI prior, REVEL) does not apply to an intronic variant; BayesDel is uncalibrated (no verified published threshold).
BP4: not_met. VCEP BP4 requires SpliceAI delta <= 0.1 for intronic variants (Walker et al 2023); SpliceAI max delta is 1.00, and the HCI-prior missense branch is inapplicable.
BP7: not_met. VCEP BP7 requires a synonymous variant or an intronic variant at or beyond -21/+7; this variant sits at +1 (within the canonical splice region) and has a strong predicted splice impact (max delta 1.00).
Population-frequency evidence for MSH2 c.2005+1G>A (NM_000251.3) under the InSiGHT MSH2 VCEP v2.0 framework: the variant is absent (AF = 0) from gnomAD v4.1 (GRCh38), gnomAD v2.1 (GRCh37), and gnomAD-Canada v1.0.
BA1 not met: AF 0 < 0.001 threshold for gnomAD v4 Grpmax filtering allele frequency (Stand Alone).
BS1 not met: AF 0 < 0.0001 lower bound of the BS1 range (Strong).
PM2 met at supporting strength: AF < 0.00002 (absent) in gnomAD v4, per VCEP PM2 rule; corroborated by ClinVar SCV001233145 population-absence signal.
BS2 not assessed: no in-trans co-occurrence with a known pathogenic MSH2 variant, no phase confirmation, and no proband phenotype/age data in the case bundle.
No disease-cohort frequencies (e.g., variant counts in Lynch syndrome family cohorts) were used as population-frequency evidence, which would be a threshold artifact.
No criteria match.
Met · 4
PVS1StrongMet (Strong): canonical +1 splice-donor variant predicted to skip in-frame exon 12 (SpliceAI delta 1.00), deleting a functionally critical ~82-amino-acid region. Not upgraded to Very Strong because no RNA assay confirmed the splice defect.
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Reasoning
NM_000251.3(MSH2):c.2005+1G>A is a canonical +1 splice donor variant (intron 12, IVS12+1; VariantValidator reports exon 12i for both start and end exon). Governing framework is the ClinGen InSiGHT MSH2 VCEP v2.0 (cspec, precedence rank 1). Under its PVS1 rules, IVS+1/+2 variants qualify for PVS1 based on the frame consequence of exon skipping or cryptic splice-site use. RefSeq NM_000251.3 exon structure (CDS 37..2841, NP_000242.1) shows exon 12 spans coding c.1760-c.2005 = 246 nt; 246 mod 3 = 0, so exon 12 is IN-FRAME: skipping it produces an in-frame deletion of ~82 amino acids (residues ~587-669), not a frameshift/PTC, so NMD is not expected and the PVS1 Very Strong branch (frameshift + NMD) does not apply. SpliceAI (max delta 1.00; DS_DL 1.0 donor loss; DS_DG 0.74 cryptic donor gain 30 nt into intron 12) predicts only in-frame outcomes (exon 12 skipping, or 30-nt intron retention = in-frame 10-aa insertion), consistent with no NMD. The deleted region is functionally critical: UniProt P43246 (MSH2_HUMAN) annotates the EXO1-interaction region at residues 601-671 and the ATP-binding (Walker A) site at residues 669-676 (Lys675; K675R mutagenesis abolishes DNA repair function), both of which lie within the exon 12-encoded segment, and this is not a repetitive/dispensable region. Therefore the VCEP rule applies: 'Variants at IVS+/-1 or IVS+/-2 where exon skipping or use of a cryptic splice site preserves reading frame and the altered region is critical to protein function' -> PVS1_Strong. PVS1 (Very Strong) via the confirmed-splice-defect branch is not met because no patient-derived mRNA/minigene assay data is present in the case bundle. Germline LoF is an established disease mechanism for MSH2 (VCEP PVS1 eligibility gate: eligible).
Rule
InSiGHT MSH2 VCEP v2.0 PVS1 (Strong): 'Variants at IVS+/-1 or IVS+/-2 where exon skipping or use of a cryptic splice site preserves reading frame and the altered region is critical to protein function. Not to be combined with PP3 and not to be used for a confirmed splice defect.'
Evidence considered
cspec (ClinGen InSiGHT MSH2 VCEP v2.0, doc 1577628936): PVS1 rule for IVS+/-1/IVS+/-2 - exon skipping/cryptic splice that disrupts reading frame with predicted NMD = PVS1; preserves reading frame with critical region = PVS1_Strong; preserves reading frame without critical region = PVS1 not used; confirmed splice defect branch requires patient mRNA assays
spliceai (SpliceAI Lookup for 2-47702410-G-A): max delta 1.00; DS_DL 1.0 (canonical donor loss), DS_DG 0.74 (cryptic donor gain at +30), DS_AL 0.01, DS_AG 0 - predicted consequences are in-frame, no NMD
UniProt P43246 (MSH2_HUMAN) domain annotation: REGION 601..671 = interaction with EXO1; BINDING 669..676 = ATP (Walker A motif, includes Lys675; MUTAGEN 675 K->R = complete loss of DNA repair function) - exon 12-encoded region is functionally critical
VariantValidator (prefetch.json): c.2005+1G>A maps to exon 12i (intron 12 donor), canonical splice consensus, MANE Select transcript NM_000251.3
Still missing
No patient-derived mRNA/cDNA assay data (with or without NMD inhibition) is available to confirm the actual splicing outcome (exon 12 skipping vs. cryptic donor usage at intron 12 +30); PVS1_Strong rests on the VCEP in silico IVS+/-1/+/-2 rule plus SpliceAI (DS_DL 1.0). RNA studies would confirm the in-frame nature of the aberrant transcript and could support the confirmed-splice PVS1 (Very Strong) branch only if no full-length transcript is produced and a functional domain is disrupted.
The InSiGHT MSH2 VCEP v2.0 Appendix (in-frame/out-of-frame exon list and the 'critical to protein function' footnote b) was not included in the case bundle; exon-frame and region-criticality conclusions were instead established from the RefSeq NM_000251.3 exon structure and UniProt P43246 domain annotations.
PM2SupportingMet (Supporting): absent from gnomAD v4.1 (AF = 0), below the <1-in-50,000 (<0.00002) allele-frequency threshold.
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Reasoning
InSiGHT MSH2 VCEP v2.0 PM2 (Supporting) is met when the allele frequency is absent/extremely rare (< 0.00002, < 1 in 50,000 alleles) in the gnomAD v4 dataset. Direct lookups report c.2005+1G>A (chr2-47475271-G-A) as absent (AF = 0) from gnomAD v4.1 (GRCh38), with corroborating absence in gnomAD v2.1 (GRCh37) and gnomAD-Canada v1.0 (HostSeq genomes). Absence on two independent builds and two datasets reduces the risk of a coordinate/build or coverage artifact at this canonical splice donor position. The ClinVar submission SCV001233145 (Labcorp Genetics/Invitae) independently recorded a population signal that the variant is not present in population databases (gnomAD), consistent with the direct lookups. The VCEP applies PM2 at supporting strength (the only listed PM2 rule is Supporting, and InSiGHT pilot classifications use PM2_supporting for MSH2 canonical splice variants). PM2 is therefore met at supporting strength.
Rule
Absent/extremely rare allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4 dataset
Evidence considered
Absent from gnomAD v4.1 (evidence.json GNOMAD_V4_1; chr2-47475271-G-A, gnomad_r4, search_status: absent)
Absent from gnomAD v2.1 (evidence.json GNOMAD_V2_1; 2-47702410-G-A, gnomad_r2_1, search_status: absent)
Absent from gnomAD-Canada v1.0 (evidence.json GNOMAD_CANADA_V1; 2-47475271-G-A, search_status: absent)
ClinVar submission SCV001233145 (Labcorp Genetics/Invitae, Pathogenic, 2025-05-05) PM2 evidence signal: 'this variant is not present in population databases (gnomad no frequency)'
PM2 rule (InSiGHT MSH2 VCEP v2.0, cspec): Absent/extremely rare allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4 dataset
Still missing
gnomAD absence is recorded as search_status 'absent' for the exact variant ID; per-position allele counts and coverage metrics were not captured in source_data (screenshots available), though absence on two independent builds/datasets mitigates coverage-artifact risk
PP4SupportingMet (Supporting): one MSI-H colorectal tumor in a documented carrier (PMID:16142001, 6-marker panel) satisfies the VCEP PP4_Supporting rule.
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Reasoning
PMID:16142001 (Becouarn et al., prospective multicentric study, Association Aquitaine Gastro) reports the exact variant in its mutation table: MSH2, intron 12, IVS12+1 G>A (i.e., c.2005+1G>A), splicing consequence, patient no. 2, tumor microsatellite status MSI-H, IHC not performed, family meets Amsterdam criteria. MSI was assessed with a 6-marker panel (BAT25, BAT26, BAT40, LmycVpA, D16S512, D16S515) and MSI-H defined as neo-alleles at >=2 markers, which is within the VCEP PP4 requirement of a standard panel of 5-10 markers. One CRC MSI-H tumor in a carrier of the variant satisfies the InSiGHT MSH2 v2.0 PP4 Supporting rule ('1 CRC/Endometrial MSI-H tumor using a standard panel of 5-10 markers... and/or loss of MMR protein expression consistent with the variant location'); IHC was not performed, which is permitted since MSI-H alone suffices. Only supporting strength is reached because a single tumor is documented; >=3 independent MSI-H tumors in >=2 families would be required for PP4_Strong.
Rule
InSiGHT MSH2 VCEP v2.0 PP4 Supporting: '1 CRC/Endometrial MSI-H tumor using a standard panel of 5-10 markers or tumor genome and/or loss of MMR protein expression consistent with the variant location. MSI-H tumor with inconsistent protein expression does not meet PP4.'
Evidence considered
PMID:16142001
cspec
Still missing
Only one MSI-H tumor in one family is documented for the exact variant (PMID:16142001); MSI/IHC data for additional independent tumors or families would be needed to upgrade PP4 beyond Supporting.
IHC (MSH2/MSH6) was not performed in the reported patient; IHC evidence consistent with MSH2 loss would strengthen the phenotype-specificity argument.
Expert panel International Society for Gastrointestinal Hereditary Tumours (InSiGHT) classified as Likely pathogenic.
Rule
Global PP5/BP6 rule: exact-variant ClinVar expert-panel classification (3-star, reviewed by expert panel) Pathogenic/Likely pathogenic -> PP5 at supporting strength; ordinary laboratory submissions and aggregate labels never trigger PP5.
Evidence considered
clinvar
ClinVar expert panel classification
Still missing
The InSiGHT VCEP v2.0 marks PP5 'Not Applicable'; the global ClinVar 3-star expert-panel rule overrides this for counting, but any downstream combination engine that honors the VCEP NA flag must be reconciled to avoid dropping PP5.
BA1Not met: allele frequency 0 in gnomAD v4, far below the >=0.001 (0.1%) BA1 threshold.
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Reasoning
InSiGHT MSH2 VCEP v2.0 BA1 (Stand Alone) requires gnomAD v4 Grpmax filtering allele frequency >= 0.001 (0.1%) and exclusion of the variant as a founder pathogenic variant. Direct gnomAD lookups report the exact variant chr2-47475271-G-A as absent (search_status 'absent', AF = 0) in gnomAD v4.1 (GRCh38) and also absent in gnomAD v2.1 (GRCh37, 2-47702410-G-A). AF = 0 is far below the 0.001 threshold, so BA1 cannot be met regardless of founder status; the founder-exclusion clause is only relevant once the AF threshold is reached. No population-frequency or threshold artifact applies.
Rule
GnomAD v4 Grpmax filtering allele frequency >= 0.001 (0.1%) and variant is excluded as founder pathogenic variant.
Evidence considered
Absent from gnomAD v4.1 (evidence.json GNOMAD_V4_1; direct variant lookup chr2-47475271-G-A, dataset gnomad_r4, GRCh38, search_status: absent)
Absent from gnomAD v2.1 (evidence.json GNOMAD_V2_1; direct variant lookup 2-47702410-G-A, dataset gnomad_r2_1, GRCh37, search_status: absent)
BA1 rule (InSiGHT MSH2 VCEP v2.0, cspec): GnomAD v4 Grpmax filtering allele frequency >= 0.001 (0.1%) and variant is excluded as founder pathogenic variant.
BS1Not met: absent from gnomAD (AF = 0), below the >=0.0001 (0.01%) lower bound of the BS1 range.
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Reasoning
InSiGHT MSH2 VCEP v2.0 BS1 (Strong) requires gnomAD v4 Grpmax filtering allele frequency >= 0.0001 (0.01%) and < 0.001, with exclusion as founder pathogenic variant. The variant is absent from gnomAD v4.1 (AF = 0), which is below the 0.0001 lower bound of the BS1 range, so BS1 is not met. Absence on two independent builds (v4.1 GRCh38 and v2.1 GRCh37) makes a build/coordinate artifact unlikely; the variant is also absent from gnomAD-Canada v1.0 (HostSeq genomes).
Rule
GnomAD v4 Grpmax filtering allele frequency >= 0.0001 and < 0.001 (0.01-0.1%) and variant is excluded as founder pathogenic variant.
Evidence considered
Absent from gnomAD v4.1 (evidence.json GNOMAD_V4_1; chr2-47475271-G-A, gnomad_r4, search_status: absent)
Absent from gnomAD v2.1 (evidence.json GNOMAD_V2_1; 2-47702410-G-A, gnomad_r2_1, search_status: absent)
Absent from gnomAD-Canada v1.0 (evidence.json GNOMAD_CANADA_V1; 2-47475271-G-A, search_status: absent)
BS1 rule (InSiGHT MSH2 VCEP v2.0, cspec): GnomAD v4 Grpmax filtering allele frequency >= 0.0001 and < 0.001 (0.01-0.1%) and variant is excluded as founder pathogenic variant.
BP4Not met: SpliceAI max delta 1.00 far exceeds the <=0.1 no-splice-impact threshold.
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Reasoning
Under the InSiGHT MSH2 VCEP v2.0, BP4_Supporting requires either a missense variant with HCI prior probability <0.11 (not applicable: c.2005+1G>A is intronic, and the HCI prior lookup returned variant_not_in_hci_table) OR an intronic/synonymous variant for which SpliceAI predicts no splicing impact with delta score <= 0.1 (as per Walker et al 2023). SpliceAI reports max delta = 1.00 (DS_DL 1.0, DS_DG 0.74) for this variant, far exceeding the <= 0.1 threshold; the prediction is instead strongly indicative of splice impact at the canonical donor. BP4 is therefore not met. BayesDel score 0.66 is not usable for BP4 (no verified published threshold).
Rule
InSiGHT MSH2 VCEP v2.0 BP4 (Supporting): 'Missense variant with HCI-prior probability of pathogenicity <0.11 ... OR For intronic and synonymous variants: SpliceAI predicts no splicing impact with delta score <= 0.1 as per Walker et al 2023.'
Evidence considered
SpliceAI lookup (spliceailookup.broadinstitute.org) for NM_000251.3:c.2005+1G>A: max delta score = 1.00 (DS_DL = 1.0 loss of donor, DS_DG = 0.74)
InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936) BP4 rule: 'For intronic and synonymous variants: SpliceAI predicts no splicing impact with delta score <= 0.1 as per Walker et al 2023' (Walker et al 2023, Am J Hum Genet 110(7):1046-1067, PMID 37352859, cited within the VCEP rule text)
Local HCI prior lookup (vcep_hci_priors_msh2): c.2005+1G>A not in table (reason: variant_not_in_hci_table); HCI priors apply to missense substitutions only
BayesDel: score 0.66 retrieved from local lookup (BayesDel_170824_noAF_chr2.gz) but no verified published threshold is available to this pipeline; treated as not_available
BP6Not met: the only expert-panel ClinVar classification (InSiGHT, 3 stars) is Likely pathogenic, not benign.
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Reasoning
BP6 requires an exact-variant ClinVar expert-panel classification of Benign/Likely benign. The only expert-panel classification for NM_000251.3(MSH2):c.2005+1G>A is the InSiGHT panel's 'Likely pathogenic' (SCV000107361, reviewed by expert panel, 3 stars), which is a pathogenic-direction classification and cannot trigger BP6. No benign/likely-benign expert-panel assertion exists for this variant in ClinVar, and the InSiGHT VCEP additionally marks BP6 'Not Applicable for this VCEP'. Therefore BP6 is not met.
Rule
Global PP5/BP6 rule: BP6 applies only for an exact-variant ClinVar expert-panel classification of Benign/Likely benign at supporting strength; the InSiGHT VCEP v2.0 also marks BP6 Not Applicable.
BP7Not met: position +1 lies inside the canonical splice region, not at or beyond +7, and SpliceAI predicts strong splice impact.
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Reasoning
Under the InSiGHT MSH2 VCEP v2.0, BP7_Supporting applies to 'a synonymous (silent) or intronic variant at or beyond -21/+7 (5'/3' exonic)'. c.2005+1G>A is an intronic variant at position +1 of the intron, i.e. inside the canonical splice region (+1 to +7), not at or beyond +7, so the positional requirement is not met. Furthermore, SpliceAI predicts strong splice impact (max delta = 1.00), the opposite of the no-impact expectation underlying BP7. BP7 is therefore not met. The variant is not synonymous.
Rule
InSiGHT MSH2 VCEP v2.0 BP7 (Supporting): 'A synonymous (silent) or intronic variant at or beyond -21/+7 (5'/3' exonic).'
Evidence considered
InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936) BP7 rule: 'A synonymous (silent) or intronic variant at or beyond -21/+7 (5'/3' exonic). Variants may satisfy both BP7 and BP4.'
SpliceAI lookup (spliceailookup.broadinstitute.org) for NM_000251.3:c.2005+1G>A: max delta score = 1.00 (DS_DL = 1.0 loss of donor, DS_DG = 0.74); variant position is +1 of the intron (canonical donor), within the +1..+7 window
PS2Not assessed: no de novo occurrence or parental testing is reported for this variant in ClinVar or the literature.
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Reasoning
Governing framework is the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification for MSH2 v2.0 (cspec), which applies PS2 via a de novo points system: confirmed de novo (maternity AND paternity confirmed) with MMR-deficient LS spectrum tumor = 2 points/proband; confirmed de novo with LS spectrum tumor but no tumor MSI/IHC data = 1 point/proband; assumed de novo with maternity and/or paternity unconfirmed = 0.5 points/proband; >=4 points = Very Strong, 2-3.5 = Strong, 1-1.5 = Moderate, 0.5 = Supporting. No proband-level de novo evidence exists for this variant in any source in the case bundle: the ClinVar record (VCV000090835, 5 submissions incl. InSiGHT expert panel) reports no de novo occurrence and no parental testing; the literature_pass contains no segregation/de novo-themed paper reporting the exact variant; and full-text review confirms the exact variant c.2005+1G>A is not mentioned in any available publication (PMID:15849733 reports different alleles at the same position, c.2005+1G>T and c.2005+2T>C, with no segregation data). De novo status, parental confirmation, and proband phenotype consistency therefore cannot be scored.
Rule
PS2 (InSiGHT MSH2 VCEP v2.0): de novo points - Very Strong >=4 points; Strong 2-3.5 points; Moderate 1-1.5 points; Supporting 0.5 points. Confirmed de novo (maternity+paternity) with MMR-deficient LS tumor = 2 pts/proband; confirmed de novo with LS tumor, no tumor data = 1 pt/proband; assumed de novo, parentage unconfirmed = 0.5 pts/proband.
Evidence considered
InSiGHT MSH2 VCEP v2.0 PS2 rule text and instructionsToUse (cspec): de novo points system with maternity/paternity confirmation and tumor phenotype requirements
ClinVar VCV000090835 submission data (clinvar): no submission reports de novo occurrence, parental testing, or segregation
PMID:15849733 full text consulted: reports c.2005+1G>T (splice defect, n=1 family) and c.2005+2T>C (n=1 family) at the same splice donor position, but NOT the exact variant c.2005+1G>A and with no proband/parental testing detail
Still missing
No proband reported with this variant; de novo occurrence status unknown
No parental testing results (maternity/paternity confirmation or exclusion) available for any carrier
No MSI/IHC/methylation tumor phenotype data linked to a proband carrying this variant, as required to weight PS2 points
PS2 de novo points cannot be computed (0 points of evidence)
PS3Not assessed: no variant-specific functional assay result exists; the only published report documents an MSI-H tumor, a phenotype observation rather than a functional test.
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Reasoning
Governing framework is the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification for MSH2 v2.0 (cspec, doc 1577628936), in which PS3 requires variant-level functional evidence: calibrated functional assays with functional odds for pathogenicity >18.7 (Strong), >4.3 and <=18.7 (Moderate), or >2.08 and <=4.3 (Supporting); Moderate is also met by an MMR function defect following the VCEP functional assay flowchart or by monoallelic expression with complete loss of expression (<10% of wild-type in cDNA without puromycin). No variant-specific functional assay result exists for NM_000251.3(MSH2):c.2005+1G>A. The SVI-curated catalog of validated MMR assays (vcep_functional_assay_svi_documentation_mmr; CIMRA cell-free MMR repair with <23% abnormal threshold for MSH2 per Drost et al. 2019 PMID 30504929, chemical-selection LOF score >0.4 per Jia/Scott PMID 33357406/36550560, full-length transcript allelic loss <=10% per Morak et al. 2019 PMID 31332305, MNNG survival per Bouvet et al. 2019 PMID 30998989, plus four Thompson et al. 2013 PMID 24362816 assays) contains no result for this variant. The only variant-specific literature report (PMID:16142001, Becouarn et al. 2005, Table II) documents the variant in a patient with an MSI-H tumor, IHC not performed and Amsterdam-positive family history — a tumor phenotype observation (PP4-type evidence), not a functional assay of the variant, and no RNA/cDNA analysis was performed. PMID:15849733 (Mangold et al. 2005) reports different alleles at the same position (c.2005+1G>T, c.2005+2T>C) with r.? (RNA not assessed), providing no functional data; PMID:24362816 (Thompson et al. 2014) states canonical splice-site substitutions fell predominantly in Class 4 'due to lack of functional RNA analyses'. Evidence is therefore insufficient to apply PS3 at any strength; the criterion is not met on current evidence.
Evidence considered
InSiGHT MSH2 VCEP v2.0 CSPEC (cspec, doc 1577628936): PS3 strength thresholds are calibrated functional odds for pathogenicity >18.7 (Strong), >4.3 and <=18.7 (Moderate, also MMR function defect per flowchart or monoallelic expression <10% of wild-type in cDNA without puromycin), >2.08 and <=4.3 (Supporting); odds calibration framework per Tavtigian et al. 2018, PMID 29300386, as referenced by the CSPEC.
Functional-assay-SVI-documentation-MMR.xlsx (vcep_functional_assay_svi_documentation_mmr): nine validated MMR assays with thresholds (e.g., CIMRA cell-free repair <23% abnormal for MLH1/MSH2, Drost et al. 2019 PMID 30504929 and Drost et al. 2020 PMID 31965077; LOF score >0.4, Jia/Scott PMID 33357406/36550560; FLT cDNA allelic loss <=10%, Morak et al. 2019 PMID 31332305; MNNG survival >45.54% abnormal for MSH2, Bouvet et al. 2019 PMID 30998989); none reports a result for c.2005+1G>A.
PMID:16142001 (Becouarn et al. 2005): reports MSH2 IVS12+1 G>A (c.2005+1G>A) in one patient with MSI-H tumor, IHC not performed, Amsterdam-positive family history; tumor phenotype observation only, no variant-specific functional assay or RNA data.
PMID:15849733 (Mangold et al. 2005): lists c.2005+1G>T and c.2005+2T>C at the same position as 'Splice defect' with r.? (RNA not assessed); different alleles from the index variant and no functional data; c.2005+1G>A itself is not listed.
PMID:24362816 (Thompson et al. 2014): InSiGHT VIC classification of 2,360 MMR variants states canonical dinucleotide splice-site substitutions fell predominantly in Class 4 due to lack of functional RNA analyses.
PMID:16199547 (Baralle & Baralle 2005): general splicing review consulted for splice-mechanism context; contains no variant-specific functional data for c.2005+1G>A.
Still missing
No calibrated functional assay result (functional odds for pathogenicity) for c.2005+1G>A in any of the nine SVI-documented MMR assays (e.g., CIMRA repair capacity, chemical-selection LOF, cell survival, complementation/expression assays).
No mRNA/cDNA analysis of the variant allele (no patient RNA with/without NMD block, no minigene assay, no allelic expression or full-length transcript data) to support PS3 Moderate via monoallelic expression <10% of wild-type.
InSiGHT LOVD microattribution data may hold unpublished functional/RNA results for this variant not captured in this case bundle; if obtainable, PS3 should be re-evaluated.
No flowchart-based MMR function defect assessment (Functional-assay-flowchart.pdf) was possible because no historic functional assay was performed for this variant.
PM3Not assessed: no second pathogenic MSH2 variant in trans (or of unknown phase) in a CMMRD-consistent patient is reported for this variant.
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Reasoning
Governing framework is the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification for MSH2 v2.0 (cspec, doc 1577628936), which redefines PM3 as: co-occurrence of the variant with a known pathogenic/likely pathogenic (P/LP) sequence variant in the same gene in a patient with clinical features consistent with constitutional mismatch repair deficiency (CMMRD) as per Aronson et al 2022 and the VCEP 'Table for CMMRD diagnosis' scoring table (vcep_table_for_cmmrd_diagnosis); scoring is 1.0 point per case with the second P/LP variant confirmed in trans and 0.5 points per case with phase unknown, summed across cases (>=4 points Very Strong, 2-3.5 Strong, 1-1.5 Moderate, 0.5 Supporting). No evidence in the case bundle satisfies any component of this rule for c.2005+1G>A: (1) no ClinVar submission (VCV000090835, variation IDs 90835/1049378/90836; 5 submissions) reports a second MSH2 variant, zygosity, or phase for any proband; (2) no CMMRD-consistent clinical features (Aronson et al 2022 criteria) are documented in any source; (3) the exact variant c.2005+1G>A appears in none of the 7 available full-text papers in the bundle (search of all publications for c.2005 / IVS12 / genomic coordinates returned no match for the queried allele; PMID 15849733 reports only the different allele c.2005+1G>T at the same +1 donor nucleotide, in single heterozygous Lynch syndrome families with no biallelic case); (4) gnomAD v2.1/v4.1/gnomAD-Canada all report the variant absent, so no population-based homozygous/biallelic signal exists either. PM3 is therefore not assessable: the required observation (variant in trans, or phase-unknown, with a second P/LP MSH2 variant in a CMMRD-consistent patient) is entirely absent from the evidence bundle. No evidence of biallelic (CMMRD) observations for this variant was found; a human review with access to InSiGHT LSD/LOVD records listing phase-confirmed compound-heterozygous CMMRD cases would be needed to apply this criterion.
Rule
PM3 (InSiGHT MSH2 VCEP v2.0): Co-occurrence with a known pathogenic/likely pathogenic sequence variant in the same gene in a patient with clinical features consistent with CMMRD as per Aronson et al 2022 (refer to Table for CMMRD diagnosis.pdf). Points: P/LP in trans = 1.0 point; P/LP phase unknown = 0.5 points; sum all cases. Strengths: >=4 points Very Strong; 2-3.5 points Strong; 1-1.5 points Moderate; =0.5 points Supporting.
Evidence considered
InSiGHT MSH2 VCEP v2.0 (cspec) PM3 rule: co-occurrence with known P/LP variant in same gene in CMMRD-consistent patient; 1.0 point if in trans, 0.5 points if phase unknown, summed across cases; >=4 points Very Strong, 2-3.5 Strong, 1-1.5 Moderate, 0.5 Supporting
VCEP Table-for-CMMRD-diagnosis.pdf (vcep_table_for_cmmrd_diagnosis): scoring table referenced by the PM3 rule for CMMRD-consistent clinical features; no patient-level data in bundle maps to it
ClinVar VCV000090835 (clinvar): 5 submissions (3 Pathogenic, 1 Likely pathogenic, 1 InSiGHT expert panel Likely pathogenic); none report a second MSH2 variant, zygosity, or phase for any proband
gnomAD v2.1, v4.1, gnomAD-Canada (gnomad_v2, gnomad_v4, gnomad_canada): variant absent from all populations; no biallelic signal available
Exhaustive search of all 7 full-text publications in the bundle for the exact variant (c.2005+1G>A, IVS12+1G>A, c.2005, genomic coordinates 2-47702410-G-A / chr2-47475271-G-A): only PMID 15849733 contains any c.2005* entry and it is the different allele c.2005+1G>T (plus c.2005+2T>C), each seen in a single heterozygous Lynch syndrome family, n=1, with no CMMRD/biallelic observation
Still missing
No documented CMMRD-consistent patient carrying c.2005+1G>A together with a second P/LP MSH2 variant (no biallelic/compound-heterozygous observation in any source in the bundle)
No phase information (in trans vs in cis vs unknown) available for any observation of c.2005+1G>A; phase confirmation by parental/offspring testing would be required per VCEP rule
No full-text publication in the bundle contains the exact variant c.2005+1G>A, so no literature-based biallelic case could be scored
PP1Not assessed: no pedigree or segregation data exist for this variant, so no co-segregation likelihood ratio could be computed.
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Reasoning
Governing framework (InSiGHT MSH2 VCEP v2.0, cspec) specifies PP1 by combined Bayes likelihood ratio from co-segregation: LR >18.7 in >=2 families = Strong; >4.3 and <=18.7 = Moderate; >2.08 and <=4.3 = Supporting (COOL v3 segregation tool recommended). No segregation data are available for this variant: no pedigrees, meioses counts, affected/unaffected relative genotypes, or segregation likelihood ratios appear in the ClinVar record, case summary, prefetch, evidence, or literature-pass artifacts, and no available full text reports the exact variant in a family context (PMID:15849733 lists different alleles at the same position in a mutation-spectrum table with no family segregation detail; PMID:24362816 InSiGHT 5-tier classification paper does not include this variant). A Bayes LR cannot be computed; PP1 is not met on the available evidence.
Rule
PP1 (InSiGHT MSH2 VCEP v2.0): Co-segregation with disease in pedigree(s) with combined Bayes Likelihood Ratio >18.7 in >=2 families = Strong; >4.3 and <=18.7 = Moderate; >2.08 and <=4.3 = Supporting.
Evidence considered
InSiGHT MSH2 VCEP v2.0 PP1 rule text (cspec): Bayes LR thresholds >18.7 (Strong, >=2 families), >4.3-18.7 (Moderate), >2.08-4.3 (Supporting)
ClinVar VCV000090835 (clinvar): submissions contain no segregation data
PMID:15849733 full text consulted for family-level data: exact variant absent; only c.2005+1G>T and c.2005+2T>C listed in mutation spectrum table, no segregation analysis
PMID:24362816 full text (InSiGHT LOVD classification paper) consulted: variant c.2005+1G>A not present in the reported variant set
Still missing
No pedigree data for any carrier family (no segregation counts, no meioses)
No Bayes likelihood ratio computable from available evidence
No affected-carrier / unaffected-noncarrier concordance data reported in ClinVar submissions or literature
BS2Not assessed: no proband or family genotype data show in-trans co-occurrence with a known pathogenic MSH2 variant.
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Reasoning
InSiGHT MSH2 VCEP v2.0 BS2 (Strong) requires documented co-occurrence in trans of the variant with a known pathogenic MSH2 sequence variant in a patient with colorectal cancer after age 45 (or another Lynch syndrome cancer above the median age of onset for that cancer in LS), without clinical manifestations of CMMRD per Aronson et al 2022, with phase confirmed by parental/offspring testing. The case-evidence bundle contains no proband or family genotype data, no second-pathogenic-variant co-occurrence observation, and no phase information for c.2005+1G>A; none of the reviewed ClinVar submissions or available full-text papers report an in-trans observation for this variant. Evidence is therefore insufficient to evaluate BS2, and the criterion is returned not_assessed pending such data.
Rule
Co-occurrence in trans with a known pathogenic sequence variant in the same gene in a patient with colorectal cancer after age 45 (or other LS cancer above the median age of onset for that cancer in LS), and who has no previous or current evidence of clinical manifestations of CMMRD as per Aronson et al 2022 (Refer to 'Table for CMMRD diagnosis.pdf'). Confirmation of phase requires testing of parents or offspring.
Evidence considered
BS2 rule (InSiGHT MSH2 VCEP v2.0, cspec): Co-occurrence in trans with a known pathogenic sequence variant in the same gene in a patient with colorectal cancer after age 45 (or other LS cancer above the median age of onset for that cancer in LS), and who has no previous or current evidence of clinical manifestations of CMMRD as per Aronson et al 2022 (Refer to 'Table for CMMRD diagnosis.pdf'). Confirmation of phase requires testing of parents or offspring.
Still missing
No data on in-trans co-occurrence of c.2005+1G>A with a known pathogenic MSH2 variant in an affected proband (CRC after age 45 or LS-spectrum cancer above median LS onset age)
No parental/offspring phase testing results for this variant
No proband CMMRD-feature assessment per Aronson et al 2022 / Table for CMMRD diagnosis (only needed if an in-trans observation were present)
BS3Not assessed: no assay demonstrates normal splicing or normal MMR function; insufficient evidence was available.
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Reasoning
Under the governing InSiGHT MSH2 VCEP v2.0 CSPEC, BS3 Strong requires calibrated functional assays with functional odds for pathogenicity <=0.05, or (for synonymous/intronic variants) no associated mRNA aberration (splicing or allelic imbalance) determined by laboratory assays conducted with nonsense-mediated decay inhibition; BS3 Supporting requires functional odds >0.05 and <=0.48, or variant-specific proficient function in protein and mRNA-based lab assays per the MMR functional assay flowchart. No such evidence exists for NM_000251.3(MSH2):c.2005+1G>A: no calibrated assay result, no mRNA/cDNA analysis with NMD inhibition, and no proficient-function data were identified in the case bundle or in the full texts reviewed (PMID:16142001 reports only tumor MSI-H phenotype with IHC not performed; PMID:15849733 lists different alleles at the same position with r.?; PMID:24362816 documents that canonical splice variants lacked functional RNA analyses; PMID:16199547 is a general splicing review). There is no evidence that this variant retains normal splicing or normal MMR function, so BS3 cannot be applied at any strength on current evidence.
Evidence considered
InSiGHT MSH2 VCEP v2.0 CSPEC (cspec, doc 1577628936): BS3 Strong = calibrated functional odds <=0.05 or synonymous/intronic variant with no mRNA aberration under NMD inhibition; BS3 Supporting = functional odds >0.05 and <=0.48 or variant-specific proficient function per flowchart; odds calibration framework per Tavtigian et al. 2018, PMID 29300386, as referenced by the CSPEC.
Functional-assay-SVI-documentation-MMR.xlsx (vcep_functional_assay_svi_documentation_mmr): validated MMR assay catalog reviewed; no result for c.2005+1G>A in any assay (e.g., CIMRA cell-free repair, Drost et al. 2019 PMID 30504929; FLT cDNA analysis, Morak et al. 2019 PMID 31332305).
PMID:16142001 (Becouarn et al. 2005): variant observed with MSI-H tumor and IHC not performed; provides no mRNA or proficient-function evidence and therefore cannot support BS3.
PMID:15849733 (Mangold et al. 2005): same-position variants reported with r.? (RNA not assessed); no mRNA data; cannot support BS3.
PMID:24362816 (Thompson et al. 2014): canonical splice-site substitutions lacked functional RNA analyses in the InSiGHT evidence base.
PMID:16199547 (Baralle & Baralle 2005): general splicing review; no variant-specific content.
Still missing
No mRNA splicing assay of this variant allele (patient RNA with and without NMD inhibition; RT-PCR/full-length transcript analysis) to demonstrate absence of splicing aberration or allelic imbalance.
No calibrated functional assay result (functional odds for pathogenicity <=0.05 Strong / >0.05-0.48 Supporting) for c.2005+1G>A in any SVI-documented MMR assay.
No variant-specific proficient-function data (protein- and mRNA-based lab assays) per the MMR functional assay flowchart.
InSiGHT LOVD microattribution data may contain unpublished RNA/functional results not captured in this bundle; if obtainable, BS3 should be re-evaluated.
BS4Not assessed: no pedigrees show affected non-carriers or unaffected carriers, so non-segregation could not be scored.
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Reasoning
Governing framework (InSiGHT MSH2 VCEP v2.0, cspec) specifies BS4 by lack of co-segregation: combined Bayes LR <0.05 = Strong; >0.05 and <=0.48 = Supporting. No non-segregation evidence exists for this variant: there are no pedigrees showing affected family members who do not carry the variant or unaffected carriers, no meioses counts, and no likelihood ratios in any case-bundle artifact or available publication. BS4 cannot be scored and is not met on the available evidence.
Rule
BS4 (InSiGHT MSH2 VCEP v2.0): Lack of co-segregation with disease in pedigree(s) with combined Bayes Likelihood Ratio <0.05 = Strong; >0.05 and <=0.48 = Supporting.
Evidence considered
InSiGHT MSH2 VCEP v2.0 BS4 rule text (cspec): lack of co-segregation Bayes LR <0.05 = Strong; >0.05 and <=0.48 = Supporting
ClinVar VCV000090835 (clinvar): no non-segregation or pedigree data reported in any of the 5 submissions
Still missing
No pedigree data demonstrating lack of co-segregation (no affected non-carriers or unaffected carriers reported)
No Bayes likelihood ratio for non-segregation computable from available evidence
BP5Not assessed: no MSS tumors, retained-MMR-IHC results, or BRAF/MLH1 methylation data exist for carriers of this variant.
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Reasoning
The InSiGHT MSH2 VCEP v2.0 defines BP5 (Applicable) using tumor phenotype evidence of an alternate basis for the phenotype: >=4 tumors with MSS and/or no loss of MMR protein expression and/or LS-spectrum tumor with MMR protein loss inconsistent with the variant gene (Strong), or 2-3 such tumors, or BRAF V600E / MLH1 methylation findings (Supporting). The case bundle contains no such data for carriers of c.2005+1G>A: no MSS tumors, no retained-MMR-IHC tumors, no inconsistent protein-loss tumors, and no BRAF V600E or MLH1 methylation testing results. The only tumor-level datum available (PMID:16142001) is an MSI-H tumor, which is the opposite of the MSS evidence BP5 requires. Evidence is insufficient to evaluate BP5.
Rule
InSiGHT MSH2 VCEP v2.0 BP5: Supporting = '2 or 3 tumors: CRC/Endometrial tumors with MSS and/or no loss of MMR protein expression and/or LS spectrum tumors with loss of MMR protein(s) that is inconsistent with the gene demonstrating genetic variation OR 1 BRAF V600E (Colon only)/MLH1 methylation (in LS spectrum tumor only) with MSI-H/MLH1 loss.'
Evidence considered
cspec
Still missing
No tumor MSS / retained-MMR-IHC / inconsistent-MMR-protein-loss data for carriers of this variant.
No BRAF V600E (CRC) or MLH1 promoter methylation testing data in LS-spectrum tumors for carriers of this variant.
Not applicable · 11· recorded as not applicableShow reasons ▾Hide reasons ▴PS1N/ANot applicable: PS1 applies only to missense or non-canonical splice variants; this canonical +1 splice-donor variant produces no amino-acid change.
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Reasoning
Governing framework is the ClinGen InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936). The variant NM_000251.3:c.2005+1G>A is a canonical +1 splice-donor variant (intron 12, exon boundary '12i' per VariantValidator; consequence_class canonical_splice, canonical_splice_consensus true; protein p.?), not a missense substitution. Both arms of the VCEP PS1 rule are structurally inapplicable: (1) the missense arm requires a predicted missense substitution encoding the same amino acid change as a previously established Pathogenic (or, at PS1_Moderate, Likely Pathogenic with normal RNA result and PM2_supporting) variant — no amino acid change exists for this intronic variant; (2) the splice arm is restricted to variants affecting the same NON-canonical splice nucleotide as a confirmed Pathogenic/Likely Pathogenic splice variant with similar or worse SpliceAI prediction — position c.2005+1 is a canonical splice nucleotide, not a non-canonical one. No same-nucleotide comparator (c.2005+1G>T / c.2005+1G>C) appears anywhere in the collected evidence bundle or the downloaded full texts (targeted grep for '2005+1' returned no hits). Per adjudication-consistency convention (same variant type = same criteria), canonical splice-donor variants are outside the scope of this VCEP's PS1, which is instead relevant to missense and non-canonical splice variants; canonical splice variants are handled by PVS1 in this framework.
Rule
A predicted missense substitution that encodes the same amino acid change with a different underlying nucleotide change previously established by this VCEP as Pathogenic (not a predicted or confirmed splice defect). OR Variants affecting the same non-canonical splice nucleotide as a confirmed Pathogenic splice variant with similar or worse splicing in silico prediction using SpliceAI. (PS1_Moderate: same amino acid change as a Likely Pathogenic missense variant with normal RNA result and PM2_supporting met, or same non-canonical splice nucleotide as a Likely Pathogenic splice variant.)
Evidence considered
cspec
clinvar
pvs1_variant_assessment
spliceai
Still missing
No evidence of a same-nucleotide splice comparator (c.2005+1G>T / c.2005+1G>C) was collected; this is moot for PS1 because the VCEP PS1 splice arm covers only non-canonical splice nucleotides and the missense arm requires an amino acid change (none exists for this intronic variant).
PS4VCEPNot applicable: the InSiGHT MSH2 VCEP scores tumor MSI/IHC evidence under PP4 and does not use PS4 proband counting.
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Reasoning
The governing framework is the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification for MSH2 v2.0 (CSPEC doc 1577628936), which explicitly marks PS4 as Not Applicable: 'Due to the availability of tumor IHC data for variant classification (see PP4), PS4 has not been utilized for MMR variant classification using proband counting.' No case-control enrichment study for this exact variant (NM_000251.3:c.2005+1G>A) exists in the case bundle, so PS4 cannot be met under either the VCEP or generic ACMG. The criterion is therefore not applicable rather than assessed.
VCEP rule
InSiGHT MSH2 VCEP v2.0: PS4 applicability = Not applicable (proband counting not used; tumor IHC evidence captured under PP4).
PM1VCEPNot applicable: the VCEP recognizes no MSH2 mutational hotspots usable for PM1, and this intronic variant has no amino-acid position.
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Reasoning
The governing InSiGHT MSH2 VCEP v2.0 CSPEC explicitly declares PM1 'Not applicable' for MSH2 with the stated rationale that there are no recognized mutational hot spots usable for classification and that pathogenic variants are distributed across all MMR functional domains. Additionally, the variant under review is intronic (canonical +1 splice donor, p.?), so it does not reside in any amino-acid domain position at all. There is therefore no pathway by which PM1 could be applied in this case; generic ACMG PM1 is not substituted because an applicable gene-specific specification exists and explicitly precludes its use.
VCEP rule
Not applicable for MSH2: There are no recognized mutational hot spots that could be used for classification purposes. While there are functional domains in the MMR genes, the distribution of pathogenic variants is generalized over all the domains (unpublished data).
PM4VCEPNot applicable: the VCEP does not use in-frame protein-length-change evidence, and this splice variant is not an in-frame indel.
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Reasoning
The governing framework, ClinGen InSiGHT MSH2 VCEP v2.0 (cspec, precedence rank 1), declares PM4 'Not applicable' for MSH2: instructionsToUse states 'Protein length change from an in-frame variant is not used due to lack of evidence.' All PM4 strength levels are marked not applicable. Additionally, the variant under review is a canonical splice-site variant (c.2005+1G>A), not an in-frame deletion/insertion or stop-loss variant, so the generic ACMG PM4 trigger (protein length change due to in-frame indel in a non-repeat region or stop-loss) does not apply at the variant level either. No PM4 evidence is evaluated.
VCEP rule
InSiGHT MSH2 VCEP v2.0 PM4: Not Applicable (protein length change from an in-frame variant not used due to lack of evidence)
Evidence considered
cspec (ClinGen InSiGHT MSH2 VCEP v2.0, doc 1577628936): PM4 applicability = 'Not applicable'; instructionsToUse = 'Protein length change from an in-frame variant is not used due to lack of evidence.'
PM5N/ANot applicable: PM5 requires a missense change at a residue where a different pathogenic missense exists; this splice variant produces no amino-acid change.
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Reasoning
The VCEP PM5 rule requires a missense change at an amino acid residue where a different missense change was classified by this VCEP as Pathogenic/Likely Pathogenic on the protein level (and not due to aberrant splicing), with PP3 supporting the missense change. The variant c.2005+1G>A is a canonical splice-donor variant with no protein consequence (NP_000242.1:p.?) and therefore produces no missense change at any residue. The case's PM5 comparator candidate collection (pm5_candidates) confirms this: pm5_mode = classic_same_residue_missense, eligible_for_classic_pm5_search = false because the variant consequence class (canonical_splice) is not missense, 0 same-residue candidates identified, and recommendation level = not_applicable. No same-residue missense comparator exists in the collected evidence, and none of the downloaded full texts mention this variant or nearby splice variants (targeted grep for '2005+1' returned no hits). PM5 is therefore inapplicable to this variant class.
Rule
Missense change at an amino acid residue where a different missense change was classified by this VCEP as Pathogenic on the protein level and not due to aberrant splicing. Only use PM5 if PP3 is supporting for the missense change. Use PM5_Supporting if other variant is Likely Pathogenic due to a missense alteration.
Evidence considered
cspec
pm5_candidates
Still missing
No same-residue missense comparator variants were identified in the collected evidence (pm5_candidates: 0 candidates, eligible_for_classic_pm5_search false); moot for PM5 because the variant is intronic (p.?) and the VCEP PM5 rule requires a missense change at a residue with a previously classified P/LP different missense change.
PM6VCEPNot applicable: the VCEP folds assumed-de-novo evidence into its PS2 points system rather than a separate PM6 code.
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Reasoning
The governing ClinGen InSiGHT MSH2 VCEP specification v2.0 (cspec) explicitly marks PM6 as 'Not applicable' for MSH2. The assumed-de-novo scenario that generic ACMG/AMP PM6 would cover (de novo without confirmed maternity/paternity) is instead absorbed into the VCEP PS2 points system at 0.5 points per proband. PM6 is therefore not a usable code under this framework, and no separate adjudication is performed. Independently, no assumed de novo proband data exist for this variant in any case-bundle source.
VCEP rule
PM6 (InSiGHT MSH2 VCEP v2.0): Not applicable - assumed de novo evidence is captured within the PS2 de novo points system (0.5 points per proband), not as a separate PM6 code.
Evidence considered
InSiGHT MSH2 VCEP v2.0 PM6 applicability declaration (cspec): 'Not applicable'; instructionsToUse state assumed de novo evidence (0.5 points/proband) is combined within PS2/PS2_VeryStrong
Still missing
None for PM6 itself (criterion not applicable under the governing VCEP); any future assumed-de-novo proband evidence would be scored under PS2 at 0.5 points
PP2VCEPNot applicable: the VCEP does not apply PP2 to MSH2, and this splice variant is not a missense change.
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Reasoning
The governing InSiGHT MSH2 VCEP v2.0 CSPEC explicitly declares PP2 'Not applicable' for MSH2 ('Missense variant in a gene with low rate of benign missense changes does not apply'). Independently, PP2 is a missense-specific criterion and the variant under review is a canonical splice-donor variant (p.?) with no missense change, so it could not be evaluated under PP2 regardless. Generic ACMG PP2 is not substituted because the applicable gene-specific specification explicitly precludes its use.
VCEP rule
Not applicable: Missense variant in a gene with low rate of benign missense changes does not apply.
PP3N/ANot applicable: PP3 covers non-canonical splice sites only; this canonical +1 variant's splice prediction is scored under PVS1 instead.
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Reasoning
NM_000251.3:c.2005+1G>A is an intronic variant at the canonical +1 splice-donor nucleotide. Under the governing InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936), the PP3 splice sub-rule applies only to NON-canonical splicing nucleotides (SpliceAI delta >= 0.2, as per Walker et al 2023). The predicted splice defect at this canonical position (SpliceAI max delta = 1.00; DS_DL 1.0, DS_DG 0.74) is captured by the PVS1 criterion instead, and the VCEP PVS1 rule explicitly states that canonical IVS+/-1,2 variants are 'not to be combined with PP3'. Counting this prediction toward PP3 would double-count the same SpliceAI evidence that the PVS1 group evaluates, which the group mandate forbids. The missense in-silico path is also inapplicable: the variant is intronic (no amino-acid substitution), the local HCI prior lookup (vcep_hci_priors_msh2) returned variant_not_in_hci_table (HCI priors cover missense substitutions only), and REVEL was not found for this position. BayesDel returned a score of 0.66 but has no verified published threshold available, so it is treated as not_available for PP3.
Rule
InSiGHT MSH2 VCEP v2.0 PP3 (Supporting): 'Missense variant with HCI prior probability for pathogenicity >0.68 & <=0.81 ... OR Predicted splice defect for non-canonical splicing nucleotides using SpliceAI with delta score >= 0.2 as per Walker et al 2023.' PP3 Moderate: HCI prior >0.81. PVS1 rule (canonical IVS+/-1,2): 'Not to be combined with PP3'.
Evidence considered
SpliceAI lookup (spliceailookup.broadinstitute.org) for NM_000251.3:c.2005+1G>A: max delta score = 1.00 (DS_DL = 1.0 loss of donor, DS_DG = 0.74)
InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936) PP3 rule: HCI prior >0.81 (Moderate) or >0.68-0.81 (Supporting) for missense; OR predicted splice defect for non-canonical splicing nucleotides with SpliceAI delta >= 0.2 (Supporting) as per Walker et al 2023, Am J Hum Genet 110(7):1046-1067, PMID 37352859 (cited within the VCEP rule text)
InSiGHT MSH2 VCEP v2.0 PVS1 rule: variants at IVS+/-1 or +/-2 where exon skipping/cryptic splice disrupts reading frame and is predicted to undergo NMD - 'Not to be combined with PP3'
Local HCI prior lookup (vcep_hci_priors_msh2): c.2005+1G>A not in table (reason: variant_not_in_hci_table); HCI priors apply to missense substitutions only
REVEL: not found for this intronic position (revel_v1_3 lookup, found=false)
BayesDel: score 0.66 retrieved from local lookup (BayesDel_170824_noAF_chr2.gz) but no verified published threshold is available to this pipeline; treated as not_available
BP1VCEPNot applicable: the VCEP does not apply BP1 to MSH2, and this splice variant is not a missense change.
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Reasoning
The governing InSiGHT MSH2 VCEP v2.0 CSPEC explicitly declares BP1 'Not applicable' for MSH2 ('Missense variant in a gene where only loss of function causes disease is not applicable'). Independently, BP1 is a missense-specific criterion and the variant under review is a canonical splice-donor variant (p.?) with no missense change, so it could not be evaluated under BP1 regardless. Generic ACMG BP1 is not substituted because the applicable gene-specific specification explicitly precludes its use.
VCEP rule
Not applicable: Missense variant in a gene where only loss of function causes disease is not applicable.
BP2VCEPNot applicable: the VCEP replaces BP2 with BS2 for MSH2, and no co-occurrence data exist for this variant.
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Reasoning
Under the governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification for MSH2 v2.0 (cspec, doc 1577628936), BP2 is explicitly marked 'Not Applicable' with the instruction 'BS2 is used instead.' The VCEP therefore replaces generic BP2 with BS2 (co-occurrence in trans with a known pathogenic variant in the same gene in a patient with colorectal cancer after age 45 or another LS-spectrum cancer above the median LS age of onset, and no evidence of CMMRD, per Aronson et al 2022) and with the biallelic-CMMRD code PM3. Consequently BP2 as a generic ACMG/AMP criterion is not applicable for MSH2 under this specification and must not be applied. Independently, no in-trans or in-cis co-occurrence data for c.2005+1G>A exists in the bundle (no ClinVar submission reports a second variant or phase; no full text contains the exact variant), so even a generic BP2 evaluation would have no evidence to draw on.
VCEP rule
BP2: Not Applicable (InSiGHT MSH2 VCEP v2.0) - 'BS2 is used instead.'
Evidence considered
InSiGHT MSH2 VCEP v2.0 (cspec) BP2 entry: applicability 'Not applicable', instructionsToUse 'BS2 is used instead', originalACMGSummary 'Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern'
InSiGHT MSH2 VCEP v2.0 (cspec) BS2 rule (the VCEP replacement for BP2): in-trans co-occurrence with a known pathogenic variant in a patient with CRC after age 45 (or LS-spectrum cancer above median LS age of onset) and no CMMRD manifestations; not evaluated here as BS2 is outside this group's assigned criteria, and no such observation exists in the bundle
Still missing
None for BP2 under the VCEP (criterion replaced by BS2/PM3 and marked Not Applicable); if a generic BP2 fallback were ever required, phase-confirmed co-occurrence data (in trans with a P/LP variant, or in cis) would be needed and is absent
BP3VCEPNot applicable: the VCEP does not use BP3, and this splice variant is not an in-frame indel in a repetitive region.
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Reasoning
The governing framework, ClinGen InSiGHT MSH2 VCEP v2.0 (cspec, precedence rank 1), declares BP3 'Not applicable' for MSH2: instructionsToUse states 'In-frame deletions/insertions in a repetitive region without a known function is not used.' All BP3 strength levels are marked not applicable. At the variant level, c.2005+1G>A is a canonical splice-site variant and is not an in-frame deletion/insertion located in a repetitive region without known function, so the generic ACMG BP3 trigger does not apply either. No BP3 evidence is evaluated.
VCEP rule
InSiGHT MSH2 VCEP v2.0 BP3: Not Applicable (in-frame indels in a repetitive region without known function not used)
Evidence considered
cspec (ClinGen InSiGHT MSH2 VCEP v2.0, doc 1577628936): BP3 applicability = 'Not applicable'; instructionsToUse = 'In-frame deletions/insertions in a repetitive region without a known function is not used.'
Every interpreted variant in MSH2, mapped onto the exon structure of NM_000251.3. Select a row to find it on the plot.
MSH2NM_000251.3
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in MSH2—Select a row to find it on the plot; use the link to open its page.
Protein
Location
Classification
Link
gnomAD v4.1Allele count data not recorded
gnomAD v2.1Allele count data not recorded
gnomAD-Canada v1.0Allele count data not recorded
Statements
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
SpliceAI acceptor lossat -246 bp
0.010
SpliceAI acceptor gainat +74 bp
0.000
SpliceAI donor lossat -1 bp
1.000
SpliceAI donor gainat +30 bp
0.740
Pangolin splice lossmagnitude shown
-0.870
Pangolin splice gain
0.180
Other predictors
REVEL
Not available
BayesDel
0.660
How the predictions were used
BP4Not met: SpliceAI max delta 1.00 far exceeds the <=0.1 no-splice-impact threshold.
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Reasoning
Under the InSiGHT MSH2 VCEP v2.0, BP4_Supporting requires either a missense variant with HCI prior probability <0.11 (not applicable: c.2005+1G>A is intronic, and the HCI prior lookup returned variant_not_in_hci_table) OR an intronic/synonymous variant for which SpliceAI predicts no splicing impact with delta score <= 0.1 (as per Walker et al 2023). SpliceAI reports max delta = 1.00 (DS_DL 1.0, DS_DG 0.74) for this variant, far exceeding the <= 0.1 threshold; the prediction is instead strongly indicative of splice impact at the canonical donor. BP4 is therefore not met. BayesDel score 0.66 is not usable for BP4 (no verified published threshold).
Rule
InSiGHT MSH2 VCEP v2.0 BP4 (Supporting): 'Missense variant with HCI-prior probability of pathogenicity <0.11 ... OR For intronic and synonymous variants: SpliceAI predicts no splicing impact with delta score <= 0.1 as per Walker et al 2023.'
Evidence considered
SpliceAI lookup (spliceailookup.broadinstitute.org) for NM_000251.3:c.2005+1G>A: max delta score = 1.00 (DS_DL = 1.0 loss of donor, DS_DG = 0.74)
InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936) BP4 rule: 'For intronic and synonymous variants: SpliceAI predicts no splicing impact with delta score <= 0.1 as per Walker et al 2023' (Walker et al 2023, Am J Hum Genet 110(7):1046-1067, PMID 37352859, cited within the VCEP rule text)
Local HCI prior lookup (vcep_hci_priors_msh2): c.2005+1G>A not in table (reason: variant_not_in_hci_table); HCI priors apply to missense substitutions only
BayesDel: score 0.66 retrieved from local lookup (BayesDel_170824_noAF_chr2.gz) but no verified published threshold is available to this pipeline; treated as not_available
BP7Not met: position +1 lies inside the canonical splice region, not at or beyond +7, and SpliceAI predicts strong splice impact.
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Reasoning
Under the InSiGHT MSH2 VCEP v2.0, BP7_Supporting applies to 'a synonymous (silent) or intronic variant at or beyond -21/+7 (5'/3' exonic)'. c.2005+1G>A is an intronic variant at position +1 of the intron, i.e. inside the canonical splice region (+1 to +7), not at or beyond +7, so the positional requirement is not met. Furthermore, SpliceAI predicts strong splice impact (max delta = 1.00), the opposite of the no-impact expectation underlying BP7. BP7 is therefore not met. The variant is not synonymous.
Rule
InSiGHT MSH2 VCEP v2.0 BP7 (Supporting): 'A synonymous (silent) or intronic variant at or beyond -21/+7 (5'/3' exonic).'
Evidence considered
InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936) BP7 rule: 'A synonymous (silent) or intronic variant at or beyond -21/+7 (5'/3' exonic). Variants may satisfy both BP7 and BP4.'
SpliceAI lookup (spliceailookup.broadinstitute.org) for NM_000251.3:c.2005+1G>A: max delta score = 1.00 (DS_DL = 1.0 loss of donor, DS_DG = 0.74); variant position is +1 of the intron (canonical donor), within the +1..+7 window
PP3N/ANot applicable: PP3 covers non-canonical splice sites only; this canonical +1 variant's splice prediction is scored under PVS1 instead.
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Reasoning
NM_000251.3:c.2005+1G>A is an intronic variant at the canonical +1 splice-donor nucleotide. Under the governing InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936), the PP3 splice sub-rule applies only to NON-canonical splicing nucleotides (SpliceAI delta >= 0.2, as per Walker et al 2023). The predicted splice defect at this canonical position (SpliceAI max delta = 1.00; DS_DL 1.0, DS_DG 0.74) is captured by the PVS1 criterion instead, and the VCEP PVS1 rule explicitly states that canonical IVS+/-1,2 variants are 'not to be combined with PP3'. Counting this prediction toward PP3 would double-count the same SpliceAI evidence that the PVS1 group evaluates, which the group mandate forbids. The missense in-silico path is also inapplicable: the variant is intronic (no amino-acid substitution), the local HCI prior lookup (vcep_hci_priors_msh2) returned variant_not_in_hci_table (HCI priors cover missense substitutions only), and REVEL was not found for this position. BayesDel returned a score of 0.66 but has no verified published threshold available, so it is treated as not_available for PP3.
Rule
InSiGHT MSH2 VCEP v2.0 PP3 (Supporting): 'Missense variant with HCI prior probability for pathogenicity >0.68 & <=0.81 ... OR Predicted splice defect for non-canonical splicing nucleotides using SpliceAI with delta score >= 0.2 as per Walker et al 2023.' PP3 Moderate: HCI prior >0.81. PVS1 rule (canonical IVS+/-1,2): 'Not to be combined with PP3'.
Evidence considered
SpliceAI lookup (spliceailookup.broadinstitute.org) for NM_000251.3:c.2005+1G>A: max delta score = 1.00 (DS_DL = 1.0 loss of donor, DS_DG = 0.74)
InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936) PP3 rule: HCI prior >0.81 (Moderate) or >0.68-0.81 (Supporting) for missense; OR predicted splice defect for non-canonical splicing nucleotides with SpliceAI delta >= 0.2 (Supporting) as per Walker et al 2023, Am J Hum Genet 110(7):1046-1067, PMID 37352859 (cited within the VCEP rule text)
InSiGHT MSH2 VCEP v2.0 PVS1 rule: variants at IVS+/-1 or +/-2 where exon skipping/cryptic splice disrupts reading frame and is predicted to undergo NMD - 'Not to be combined with PP3'
Local HCI prior lookup (vcep_hci_priors_msh2): c.2005+1G>A not in table (reason: variant_not_in_hci_table); HCI priors apply to missense substitutions only
REVEL: not found for this intronic position (revel_v1_3 lookup, found=false)
BayesDel: score 0.66 retrieved from local lookup (BayesDel_170824_noAF_chr2.gz) but no verified published threshold is available to this pipeline; treated as not_available
SpliceAI predicts possible splice impact for this variant (max delta score = 1.00). BayesDel score = 0.66.
9 paper records listed. 1 cited in the classification.
Cited in the classification
Value of microsatellite instability typing in detecting hereditary non-polyposis colorectal cancer. A prospective multicentric study by the Association Aquitaine Gastro.
Bécouarn Y et al. · 2005 Jun-Jul
Prospective multicentric study by the Association Aquitaine Gastro evaluating MSI typing plus immunohistochemistry to select patients for germline MMR mutation analysis. Table II lists the germline mutations identified per patient; the MSH2 intron 12 row reports IVS12+1 G>A (equivalent to NM_000251.3:c.2005+1G>A) in one patient (patient no. 2) whose tumor was MSI-H, for whom immunohistochemistry was not performed, and who had an Amsterdam-positive family history; the predicted consequence is recorded as 'splicing'. The paper performed no RNA/cDNA analysis or in vitro functional assay for this variant — the MSI-H tumor is a tumor phenotype observation, not a variant functional assay. The paper's general statement that observed mutations 'were considered to have a deleterious effect' reflects the authors' clinical judgment, not functional assay evidence.
MSH2 | 12 | IVS12+1 | G > A | splicing | 2 | MSI-H | not performed | Amsterdam (Table II row); 'The different types of mutations observed were considered to have a deleterious effect, leading to HNPCC syndrome.'
Location Table II (Tumor microsatellite instability, immunohistochemistry, family history and germline mutations), MSH2 intron 12 row, patient no. 2; extracted text lines 616-624; discussion lines 505-511.
Context Prospective multicentric French study (Association Aquitaine Gastro) of patients selected by clinical criteria (age at onset <50 years or family history of HNPCC tumors) plus tumor MSI typing and MMR immunohistochemistry, followed by germline MMR gene sequencing. Table II tabulates tumor MSI status, IHC, genealogic data and germline mutations per patient.
Other recorded publications
Spectrum and frequencies of mutations in MSH2 and MLH1 identified in 1,721 German families suspected of hereditary nonpolyposis colorectal cancer.
Mangold E et al. · 2005
Multicenter study of the MSH2/MLH1 mutation spectrum in 1,721 German families suspected of HNPCC. The mutation table lists intron 12 (IVS12) splice-site variants c.2005+1G>T and c.2005+2T>C (each in 1 family), annotated as splice defects with unknown RNA consequence (r.?). The exact allele under review, c.2005+1G>A, is NOT reported in this paper (the downloaded full text contains no c.2005+1G>A entry), so this publication cannot be cited as variant-specific evidence for c.2005+1G>A. It is documented here only as part of the audit trail for the variant search.
Splicing in action: assessing disease causing sequence changes.
Baralle D et al. · 2005
Narrative review by Baralle and Baralle on pre-mRNA splicing mechanisms and how disease-causing sequence changes disrupt splicing (exon skipping, intron retention, cryptic splice site activation, splicing regulatory elements). It provides general background on why splice-site variants require experimental verification and discusses the utility of splicing assays, but it does not mention MSH2 c.2005+1G>A or any specific MMR variant, and contains no variant-specific functional data. Consulted only as splice-mechanism context; it does not support or refute PS3/BS3 for the index variant.
These mutations can result in either complete skipping of the exon, retention of the intron, or the introduction of a new splice site within an exon or intron.
Abstract (lines 9-13 of extracted text); general review content throughout.
Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database.
Thompson BA et al. · 2014
InSiGHT 5-tier standardized classification of 2,360 unique MMR gene variants. Full text was searched for the queried variant and for segregation/proband/de novo terms; c.2005+1G>A does not appear in the variant set, and no segregation or de novo data relevant to this variant are reported.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Pathogenic (3 clinical laboratories) and as Likely pathogenic (1 clinical laboratory) and as Likely pathogenic by International Society for Gastrointestinal Hereditary Tumours (InSiGHT) (expert panel). (ClinVarID = 90835)
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 1.00). BayesDel score = 0.66.
Somatic
This variant has previously been reported in somatic cancers (COSMIC; COSV51887065, n = 1 times).
This variant was interpreted by pipeline 7.1.0.
The current version is 11.0.07.
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