About MLH1
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
MLH1 c.222T>C, p.(Asp74=)
Classification
Likely benign
Variant description:
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is likely benign. Select a step to read what it means.
Likely benign.A likely benign 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.
LYFE Sciences is an AI system, and it can make mistakes.
Criteria may be applied incorrectly, sources may be misread, and a
confident-looking classification can still be wrong.
Double-check every criterion and its underlying evidence
before relying on any call.
01The reasoning
How it was classified
The recorded framework is ClinGen MLH1 VCEP v2.0.0. 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.
Pathogenic evidence criteria: 0
Benign evidence criteria: 3
Pathogenic criteria applied · 0
No pathogenic criterion marked as applied in the recorded assessment.
Benign criteria applied · 3
BS3Supporting
BS3 · supporting
BS3_Supporting is met. An RNA splicing assay performed by a clinical diagnostic laboratory (Invitae, reported via ClinVar) indicates that NM_000249.4:c.222T>C does not significantly alter splicing. This is direct functional evidence of no splicing aberration for a synonymous variant where aberrant splicing would be the only plausible pathogenic mechanism. SpliceAI independently predicts no splicing impact (max delta 0.03). Under the VCEP BS3_Supporting rule, variant-specific proficient function in mRNA-based lab assays qualifies.
BP4Supporting
BP4 · supporting
BP4_Supporting is met. Under the VCEP rule for synonymous variants, BP4_Supporting applies when SpliceAI predicts no splicing impact with a delta score <=0.1. SpliceAI max delta for NM_000249.4:c.222T>C is 0.03, meeting this threshold. Additionally, REVEL score is 0.035 (strongly benign-leaning).
BP7Supporting
BP7 · supporting
BP7_Supporting is met. NM_000249.4:c.222T>C is a synonymous variant located at nucleotide position 15 within exon 3 (c.208-c.306). This falls within the -21 position from the acceptor splice site (positions c.208-c.228), satisfying the VCEP BP7 rule for synonymous variants at or beyond -21/+7 (5'/3' exonic). SpliceAI also predicts no splicing impact (delta 0.03). BP7 and BP4 may both be applied.
Recorded classification: Likely benign
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MLH1 Version 2.0.0 v2.0.0 criteria-combination framework: matched Rule19 (Benign.Supporting >=2) with applied criteria: BS3 supporting, BP4 supporting, BP7 supporting; maps to Likely Benign.
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
37 / 1,595,534 alleles
gnomAD v4.1: 37 / 1,595,534 alleles. Recorded AF 2.31897e-05. Recorded homozygote count 0.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 7.95684e-06; MAF= 0.00080%, 2/251356 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.75936e-05; MAF= 0.00176%, 2/113678 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
No listed criterion applied
SpliceAI score
0.030 maximum delta
Recorded SpliceAI maximum delta score: 0.030. Refer to the recorded PP3/BP4 rationale for interpretation.
ClinVar submissions
8 reported laboratory submissions
6 Likely benign · 1 Uncertain significance · 1 Benign.
Context only
ClinVar ↗
Functional evidence
Statement recorded
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
Context only
For specialists
Technical detail
ACMG/AMP criteria under ClinGen MLH1 VCEP v2.0.0, with the data and sources behind each one.
26 criteria with recorded statuses: 3 met · 5 not met · 6 not assessed · 12 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_000249.4:c.222T>C is a synonymous variant (p.Asp74=) in exon 3 of MLH1.
SpliceAI predicts no splicing impact (max delta score 0.03), satisfying BP4_Supporting under InSiGHT MLH1 VCEP v2.0.0 rules for synonymous variants.
The variant is located within the -21 exonic splice region (c.222 in exon 3, acceptor c.208), satisfying BP7_Supporting.
An RNA splicing assay performed by a clinical diagnostic laboratory indicates this variant does not significantly alter splicing, consistent with a benign functional effect (BS3_Supporting).
The variant is present in gnomAD v4.1 at a low frequency (37/1,595,534 alleles; AF=2.32e-05) that exceeds the VCEP PM2_Supporting threshold of <0.00002, therefore PM2 is not met. The frequency does not reach BS1 or BA1 thresholds.
The variant has been reported in ClinVar as Likely benign by six clinical laboratories (ClinVar ID 237333).
No evidence of pathogenicity was identified: PVS1, PS1, and PM5 are not applicable (synonymous); PS2/PM6, PP1, PP4, BS2, BS4, and BP5 lack data; PS3, PP3, BA1, and BS1 are not met.
No criteria match.
Met · 3
BS3 SupportingBS3_Supporting is met. An RNA splicing assay performed by a clinical diagnostic laboratory (Invitae, reported via ClinVar) indicates that NM_000249.4:c.222T>C does not significantly alter splicing. This is direct functional evidence of no splicing aberration for a synonymous variant where aberrant splicing would be the only plausible pathogenic mechanism. SpliceAI independently predicts no splicing impact (max delta 0.03). Under the VCEP BS3_Supporting rule, variant-specific proficient function in mRNA-based lab assays qualifies. Details ▾Hide ▴
Evidence considered
- Invitae RNA splicing assay (ClinVar): no significant alteration of splicing
- SpliceAI max delta=0.03 (no predicted splice impact).
Still missing
- Functional evidence is from a clinical laboratory summary rather than a peer-reviewed publication
- no independent replication reported.
Sources
BP4 SupportingBP4_Supporting is met. Under the VCEP rule for synonymous variants, BP4_Supporting applies when SpliceAI predicts no splicing impact with a delta score <=0.1. SpliceAI max delta for NM_000249.4:c.222T>C is 0.03, meeting this threshold. Additionally, REVEL score is 0.035 (strongly benign-leaning). Details ▾Hide ▴
Evidence considered
- SpliceAI max delta=0.03 (<=0.1
- no predicted splice impact)
- REVEL=0.035.
Sources
BP7 SupportingBP7_Supporting is met. NM_000249.4:c.222T>C is a synonymous variant located at nucleotide position 15 within exon 3 (c.208-c.306). This falls within the -21 position from the acceptor splice site (positions c.208-c.228), satisfying the VCEP BP7 rule for synonymous variants at or beyond -21/+7 (5'/3' exonic). SpliceAI also predicts no splicing impact (delta 0.03). BP7 and BP4 may both be applied. Details ▾Hide ▴
Evidence considered
- Synonymous variant at c.222
- within -21 from exon 3 acceptor (c.208)
- SpliceAI delta=0.03.
Sources
Not met · 5 · evaluated, threshold not reached
PS3 PS3 is not met. No well-established functional studies demonstrate a damaging effect for this synonymous variant. An RNA splicing assay reported by a clinical laboratory (Invitae, cited in ClinVar) indicates this variant does not significantly alter splicing, which contradicts a damaging functional effect. The variant is not listed in the MMR calibrated functional assay dataset. Details ▾Hide ▴
Evidence considered
- RNA splicing assay from Invitae (ClinVar) shows no significant splicing alteration
- absent from VCEP calibrated functional assay spreadsheet.
Still missing
- No peer-reviewed functional study specific to this variant.
Sources
PM2 PM2_Supporting is not met. Under the VCEP rule, PM2_Supporting requires an allele frequency <0.00002 (fewer than 1 in 50,000 alleles) in gnomAD v4. The variant is present in gnomAD v4.1 at an allele frequency of 2.32e-05 (37/1,595,534 alleles, grpmax FAF=2.35e-05), which exceeds the PM2_Supporting threshold. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1: AF=2.32e-05 (37/1
- 595
- 534)
- grpmax FAF=2.35e-05
- exceeds VCEP PM2_Supporting threshold of <0.00002.
Sources
PP3 PP3 is not met. Under VCEP rules, for synonymous variants, PP3_Supporting requires a SpliceAI delta score >=0.2 for non-canonical splicing nucleotides. The SpliceAI max delta score for this variant is 0.03, well below the threshold. No HCI prior score is available for synonymous variants. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta=0.03 (far below 0.2 threshold for PP3_Supporting)
- REVEL=0.035 (benign-leaning).
Sources
BA1 BA1 is not met. The VCEP rule requires a gnomAD v4 grpmax filtering allele frequency >=0.001 (0.1%). The variant has a grpmax FAF of 2.35e-05 (0.00235%), far below the BA1 threshold. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1 grpmax FAF=2.35e-05 (0.00235%)
- below BA1 threshold of >=0.001.
Sources
BS1 BS1 is not met. The VCEP rule requires a gnomAD v4 grpmax filtering allele frequency >=0.0001 and <0.001 (0.01-0.1%). The variant has a grpmax FAF of 2.35e-05 (0.00235%), below the BS1 lower bound of 0.0001. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1 grpmax FAF=2.35e-05
- below BS1 threshold lower bound of >=0.0001.
Sources
Not assessed · 6 · no assessment recorded
PS2 No de novo occurrences of NM_000249.4:c.222T>C were identified in any database or publication. Absent de novo evidence precludes application of PS2. Details ▾Hide ▴
Still missing
- No de novo reports identified in ClinVar
- PubMed
- or gnomAD de novo track.
PP1 No co-segregation data are available for this variant. No published family studies or segregation analyses mentioning NM_000249.4:c.222T>C were identified. Details ▾Hide ▴
Still missing
- No published segregation or linkage data for this variant.
Sources
25070057
PP4 No tumor MSI/IHC data specific to this variant are available. PP4 under the VCEP requires MSI-H tumor data with loss of MMR protein expression consistent with the variant location. Absent such data, PP4 cannot be assessed. Details ▾Hide ▴
Still missing
- No tumor phenotype data (MSI/IHC) available for this variant.
BS2 No data on co-occurrence in trans with a known pathogenic MLH1 variant are available. BS2 requires confirmed phase with a pathogenic variant in a patient meeting specific clinical criteria. Details ▾Hide ▴
Still missing
- No co-occurrence or phase data available.
BS4 No segregation or lack-of-segregation data are available for this variant. BS4 requires a Bayes likelihood ratio from pedigree analysis demonstrating lack of co-segregation with disease. Details ▾Hide ▴
Still missing
- No pedigree or segregation data available.
Sources
25070057
BP5 No tumor phenotype data (MSS status, MMR protein expression, BRAF/MLH1 methylation) are available for this variant. BP5 requires specific tumor characteristics inconsistent with LS. Details ▾Hide ▴
Still missing
- No tumor data (MSS/MSI
- IHC
- BRAF
- methylation) available.
Not applicable · 12· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/APVS1 is not applicable. NM_000249.4:c.222T>C is a synonymous variant (p.Asp74=) and is neither a null variant (nonsense, frameshift, canonical splice) nor predicted to result in a loss-of-function mechanism. The variant falls outside the PVS1 decision tree for MMR genes. Details ▾Hide ▴
Evidence considered
- Synonymous variant p.(Asp74=) with no predicted null effect
- PVS1 variant assessment bucket is 'other'.
Sources
pvs1_gene_contextpvs1_variant_assessmentvcep_pvs1_decisiontree_mmr
PS1 N/APS1 is not applicable. This variant is synonymous (p.Asp74=) and does not encode an amino acid change; there is no amino acid substitution to compare against a previously established pathogenic missense change. Details ▾Hide ▴
Evidence considered
- Synonymous variant with no amino acid change
- no comparator nucleotide change encoding the same amino acid exists.
Sources
PS4 VCEPPS4 is designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel VCEP for MLH1 v2.0.0. Details ▾Hide ▴
PM1 VCEPPM1 is designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel VCEP for MLH1 v2.0.0. Details ▾Hide ▴
PM5 N/APM5 is not applicable. The variant is synonymous (p.Asp74=) and does not produce a missense change. PM5 requires a missense alteration at an amino acid residue where a different missense change has been classified as Pathogenic or Likely Pathogenic. No candidate comparators were identified. Details ▾Hide ▴
Evidence considered
- Synonymous variant
- no missense residue context for PM5 comparison.
Sources
pm5_candidatescspec ↗
PM6 VCEPPM6 is designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel VCEP for MLH1 v2.0.0. Details ▾Hide ▴
PP2 VCEPPP2 is designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel VCEP for MLH1 v2.0.0. Details ▾Hide ▴
PP5 VCEPPP5 is designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel VCEP for MLH1 v2.0.0. Details ▾Hide ▴
BP1 VCEPBP1 is designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel VCEP for MLH1 v2.0.0. Details ▾Hide ▴
BP2 VCEPBP2 is designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel VCEP for MLH1 v2.0.0. Details ▾Hide ▴
BP6 VCEPBP6 is designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel VCEP for MLH1 v2.0.0. Details ▾Hide ▴
PS5 N/APS5 is not defined in the InSiGHT MLH1 VCEP v2.0.0 criteria. The corresponding PP5 criterion is explicitly Not Applicable per the VCEP. In VCEP mode, PS5 is not used. Details ▾Hide ▴
Identifiers
- Gene
- MLH1
- Transcript
- NM_000249.4
- Coding (HGVS c.)
- NM_000249.4:c.222T>C
- Protein (HGVS p.)
- NP_000240.1:p.(Asp74=)
- GRCh38
- chr3:37000969 T>C
- GRCh37
- chr3:37042460 T>C
- ClinVar
- 237333
Gene diagram
Every interpreted variant in MLH1, mapped onto the exon structure of NM_000249.4. Select a row to find it on the plot.
MLH1NM_000249.4
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 MLH1
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Select a row to find it on the plot; use the link to open its page.
| Protein | Location | Classification | Link |
|---|
gnomAD v4.1
37 / 1,595,534 alleles
AF 2.32e-05 · 0 homozygotes · FAF 2.35e-05
gnomAD v2.1
2 / 251,356 alleles
AF 7.96e-06 · 0 homozygotes · FAF 2.92e-06
gnomAD-Canada v1.0
0 / 0 alleles
AF 0 · 0 homozygotes · FAF 0
By genetic ancestry
gnomAD v4.1
AF 2.3e-05 · 37 / 1,595,534 alleles · 0 hom · FAF 2.3e-05
| European (non-Finnish)37 / 1,163,262 | 3.2e-05 |
0 alternate alleles recorded in 9 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American.
gnomAD v2.1
AF 8e-06 · 2 / 251,356 alleles · 0 hom · FAF 2.9e-06
| European (non-Finnish)2 / 113,678 | 1.8e-05 |
0 alternate alleles recorded in 7 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian.
gnomAD-Canada
AF 0 · 0 / 0 alleles · 0 hom
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 2.31897e-05; MAF= 0.00232%, 37/1595534 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.18071e-05; MAF= 0.00318%, 37/1163262 alleles, homozygotes = 0); grpmax FAF= 2.347e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 7.95684e-06; MAF= 0.00080%, 2/251356 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.75936e-05; MAF= 0.00176%, 2/113678 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
SpliceAI and Pangolin
Other predictors
- REVEL
- 0.035
- BayesDel
- Not available
How the predictions were used
BP4 SupportingBP4_Supporting is met. Under the VCEP rule for synonymous variants, BP4_Supporting applies when SpliceAI predicts no splicing impact with a delta score <=0.1. SpliceAI max delta for NM_000249.4:c.222T>C is 0.03, meeting this threshold. Additionally, REVEL score is 0.035 (strongly benign-leaning). Details ▾Hide ▴
Evidence considered
- SpliceAI max delta=0.03 (<=0.1
- no predicted splice impact)
- REVEL=0.035.
Sources
BP7 SupportingBP7_Supporting is met. NM_000249.4:c.222T>C is a synonymous variant located at nucleotide position 15 within exon 3 (c.208-c.306). This falls within the -21 position from the acceptor splice site (positions c.208-c.228), satisfying the VCEP BP7 rule for synonymous variants at or beyond -21/+7 (5'/3' exonic). SpliceAI also predicts no splicing impact (delta 0.03). BP7 and BP4 may both be applied. Details ▾Hide ▴
Evidence considered
- Synonymous variant at c.222
- within -21 from exon 3 acceptor (c.208)
- SpliceAI delta=0.03.
Sources
PP3 PP3 is not met. Under VCEP rules, for synonymous variants, PP3_Supporting requires a SpliceAI delta score >=0.2 for non-canonical splicing nucleotides. The SpliceAI max delta score for this variant is 0.03, well below the threshold. No HCI prior score is available for synonymous variants. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta=0.03 (far below 0.2 threshold for PP3_Supporting)
- REVEL=0.035 (benign-leaning).
Sources
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.035.
9 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Recorded publications
-
PMID 25070057 ↗Guidelines on genetic evaluation and management of Lynch syndrome: a consensus statement by the US Multi-society Task Force on colorectal cancer.Giardiello FM et al. · 2014No paper-specific finding is recorded.
-
PMID 25645574 ↗ACG clinical guideline: Genetic testing and management of hereditary gastrointestinal cancer syndromes.No paper-specific finding is recorded.
-
PMID 25741868 ↗Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.No paper-specific finding is recorded.
-
PMID 26467025 ↗A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.No paper-specific finding is recorded.
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PMID 11598466 ↗Practice parameters for the identification and testing of patients at risk for dominantly inherited colorectal cancer--supporting documentation.Church J et al. · 2001No paper-specific finding is recorded.
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PMID 20065170 ↗American Society of Clinical Oncology policy statement update: genetic and genomic testing for cancer susceptibility.Robson ME et al. · 2010No paper-specific finding is recorded.
-
PMID 20301390 ↗Lynch Syndrome.Adam MP et al. · 1993No paper-specific finding is recorded.
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PMID 22167527 ↗Identification of individuals at risk for Lynch syndrome using targeted evaluations and genetic testing: National Society of Genetic Counselors and the Collaborative Group of the Americas on Inherited Colorectal Cancer joint practice guideline.No paper-specific finding is recorded.
-
PMID 28492532 ↗Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.No paper-specific finding is recorded.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
37 / 1,595,534 recorded alleles
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.030
Open source ↗
ClinVar
6 Likely benign · 1 Uncertain significance · 1 Benign
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
Cancer hotspots
Captured Cancer Hotspots source record
Open source ↗
OncoKB
Captured OncoKB source record
Open source ↗
ClinGen CSpec
Captured ClinGen CSpec source record
Open source ↗
All source links
- ClinGen CSpec ↗cspec.genome.network/cspec/ui/svi/doc/1564688410
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/237333/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/3-37042460-T-C?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr3-37000969-T-C?dataset=gnomad_r4
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_000249.4%3Ac.222T…
- OncoKB ↗www.oncokb.org/gene/MLH1/D74=
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=MLH1+c.222T%3EC
- Cancer hotspots ↗www.cancerhotspots.org/
Statements for reports
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 2.31897e-05; MAF= 0.00232%, 37/1595534 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.18071e-05; MAF= 0.00318%, 37/1163262 alleles, homozygotes = 0); grpmax FAF= 2.347e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 7.95684e-06; MAF= 0.00080%, 2/251356 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.75936e-05; MAF= 0.00176%, 2/113678 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
ClinVar
This variant has been reported in ClinVar as Likely benign (6 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as Benign (1 clinical laboratory). (ClinVarID = 237333)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.035.
Functional
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
Somatic
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.