About CHEK2
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
CHEK2 c.1095+19G>A, p.?
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.
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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 CHEK2 VCEP v1.0.0. 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
BS2Supporting
BS2 · supporting
A homozygous individual for NM_007194.4:c.1095+19G>A is observed in gnomAD v4.1 (1 homozygote among 1,542,484 alleles). CHEK2 is an autosomal dominant cancer predisposition gene where biallelic pathogenic variants would be expected to cause a severe or embryonic lethal phenotype. Observation of a homozygote in a population database is inconsistent with a highly penetrant pathogenic role and supports a benign interpretation.
BP4Supporting
BP4 · supporting
Computational evidence suggests no impact on splicing. SpliceAI predicts no splice alteration with a maximum delta score of 0.00 across all categories (acceptor gain, acceptor loss, donor gain, donor loss). The variant resides at position +19 in intron 10, well outside the canonical splice consensus, consistent with a neutral intronic change.
BP6Supporting
BP6 · supporting
ClinVar reports NM_007194.4:c.1095+19G>A as Likely benign by 9 clinical laboratories and Benign by 3 clinical laboratories (Variation ID: 371849). Multiple independent clinical laboratories have reached a benign or likely benign classification, providing reputable source support for a benign interpretation.
Recorded classification: Likely benign
Hereditary Breast, Ovarian and Pancreatic Cancer Specification v1.0.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BS2 supporting, BP4 supporting, BP6 supporting; combination = 3 supporting benign, which 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
186 / 1,542,484 alleles
gnomAD v4.1: 186 / 1,542,484 alleles. Recorded AF 0.000120585. Recorded homozygote count 1.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.000166616; MAF= 0.01666%, 47/282086 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.00094827; MAF= 0.09483%, 29/30582 alleles, homozygotes = 0); grpmax FAF= 0.00067758.
gnomAD-Canada
Not available in gnomAD-Canada v1.0.
SpliceAI score
0.000 maximum delta
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
ClinVar submissions
12 reported laboratory submissions
9 Likely benign · 3 Benign.
No screenshot for this evidence
Functional evidence
Not recorded
No standalone functional evidence summary is recorded in evidence_summary.functional.
No listed criterion applied
OncoKB ↗
Somatic evidence
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
Context only
COSMIC ↗
For specialists
Technical detail
ACMG/AMP criteria under ClinGen CHEK2 VCEP v1.0.0, with the data and sources behind each one.
29 criteria with recorded statuses: 3 met · 9 not met · 7 not assessed · 10 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_007194.4:c.1095+19G>A is an intronic variant in CHEK2 located at position +19 in intron 10.
Computational evidence predicts no splicing impact: SpliceAI maximum delta score is 0.00 across all categories, consistent with a neutral intronic change (BP4_Supporting).
A homozygous individual for this variant is observed in gnomAD v4.1, which is inconsistent with a highly penetrant autosomal dominant cancer predisposition variant (BS2_Supporting).
ClinVar reports this variant as Likely benign by 9 clinical laboratories and Benign by 3 clinical laboratories (Variation ID: 371849), providing reputable source support for a benign interpretation (BP6_Supporting).
The variant is observed at population frequencies of 0.017% (gnomAD v2.1) and 0.012% (gnomAD v4.1) with the highest subpopulation frequency of 0.237% in the Middle Eastern population (gnomAD v4.1), which approaches but does not exceed the BS1 threshold of 0.3%.
No functional studies, segregation data, case-control enrichment, or variant-specific publications were identified for this variant.
Three benign supporting criteria (BP4, BP6, BS2) are met. Under generic ACMG/AMP 2015 combination rules (PMID:25741868), two or more benign supporting criteria support a Likely Benign classification.
No criteria match.
Met · 3
BS2 SupportingA homozygous individual for NM_007194.4:c.1095+19G>A is observed in gnomAD v4.1 (1 homozygote among 1,542,484 alleles). CHEK2 is an autosomal dominant cancer predisposition gene where biallelic pathogenic variants would be expected to cause a severe or embryonic lethal phenotype. Observation of a homozygote in a population database is inconsistent with a highly penetrant pathogenic role and supports a benign interpretation. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1: 1 homozygous individual observed out of 1
- 542
- 484 alleles
- CHEK2 is an autosomal dominant cancer predisposition gene
- homozygosity for a pathogenic variant would be unexpected in the general population
Still missing
- The gnomAD homozygote individual's phenotype is unknown
- gnomAD is not a confirmed healthy cohort
Sources
BP4 SupportingComputational evidence suggests no impact on splicing. SpliceAI predicts no splice alteration with a maximum delta score of 0.00 across all categories (acceptor gain, acceptor loss, donor gain, donor loss). The variant resides at position +19 in intron 10, well outside the canonical splice consensus, consistent with a neutral intronic change. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.00 (all categories: donor loss=0.00
- donor gain=0.00
- acceptor loss=0.00
- acceptor gain=0.00)
- Deep intronic position (+19) outside conserved splice region
Sources
BP6 SupportingClinVar reports NM_007194.4:c.1095+19G>A as Likely benign by 9 clinical laboratories and Benign by 3 clinical laboratories (Variation ID: 371849). Multiple independent clinical laboratories have reached a benign or likely benign classification, providing reputable source support for a benign interpretation. Details ▾Hide ▴
Evidence considered
- ClinVar Variation ID 371849: Likely benign (9 labs)
- Benign (3 labs)
- 12 clinical laboratories with concordant benign-leaning classification
- Two submitters (GeneDx
- Color Health) provided assertion criteria
Sources
Not met · 9 · evaluated, threshold not reached
PS2 No de novo data are available for NM_007194.4:c.1095+19G>A. No publications or ClinVar submissions report de novo occurrence of this variant. Details ▾Hide ▴
Evidence considered
- No de novo observations in ClinVar submissions or reviewed literature
Still missing
- No family-based de novo testing data available
PS4 No case-control enrichment data are available for NM_007194.4:c.1095+19G>A. The variant is observed in 47/282,086 alleles in gnomAD v2.1 and 186/1,542,484 alleles in gnomAD v4.1, consistent with a benign polymorphism rather than enriched in affected individuals. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1: 47 alleles
- AF=0.017%
- gnomAD v4.1: 186 alleles
- AF=0.012%
- 1 homozygote
- No published case-control studies demonstrating enrichment in affected individuals
Sources
PM1 NM_007194.4:c.1095+19G>A is a deep intronic variant located 19 bases downstream of exon 10. It does not reside in a mutational hotspot or well-established critical functional domain. No OncoKB hotspot data support pathogenic clustering at this position. Details ▾Hide ▴
Evidence considered
- Intronic position (+19) outside any functional domain
- No hotspot or cluster data indicate functional significance
PM2 PM2 requires absence or extremely low frequency in population databases. NM_007194.4:c.1095+19G>A is present in gnomAD v2.1 at AF=0.017% (47/282,086 alleles) and in gnomAD v4.1 at AF=0.012% (186/1,542,484 alleles, including 1 homozygote). While below the 0.1% threshold, the presence of a homozygous individual in an autosomal dominant cancer predisposition gene and frequencies exceeding those expected for a highly penetrant pathogenic variant argue against PM2 application. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1: 47 alleles observed (AF=0.017%)
- gnomAD v4.1: 186 alleles observed (AF=0.012%)
- gnomAD v4.1: 1 homozygote observed
- inconsistent with highly penetrant dominant cancer variant
Sources
PM6 No de novo data are available for NM_007194.4:c.1095+19G>A. No publications or ClinVar submissions report de novo occurrence with confirmed maternity and paternity. Details ▾Hide ▴
Evidence considered
- No de novo reports identified in ClinVar or literature
Still missing
- No family-based testing data available
PP3 Multiple lines of computational evidence do not support a deleterious effect. SpliceAI predicts no splice impact (max delta score = 0.00 for all categories: acceptor gain, acceptor loss, donor gain, donor loss). REVEL and BayesDel scores are not available for this intronic variant as they require missense changes. No in silico tool predicts pathogenicity. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.00 — no predicted splice alteration
- REVEL: not applicable (intronic variant)
- BayesDel: not applicable (intronic variant)
- HCI prior: not applicable (gene not supported)
Sources
PP5 PP5 requires a reputable source to have recently reported the variant as pathogenic. ClinVar classification for this variant is Likely benign (9 clinical laboratories) and Benign (3 clinical laboratories). No reputable source reports this variant as pathogenic. Details ▾Hide ▴
Evidence considered
- ClinVar: Likely benign (9 labs)
- Benign (3 labs)
- No source reports this variant as pathogenic
Sources
BA1 BA1 requires allele frequency >1% in population databases. The highest observed population frequency is 0.237% in the Middle Eastern subpopulation (gnomAD v4.1) and 0.095% in the South Asian subpopulation (gnomAD v2.1). Neither approaches the 1% stand-alone benign threshold. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1: max subpopulation AF = 0.095% (South Asian)
- gnomAD v4.1: max subpopulation AF = 0.237% (Middle Eastern)
- grpmax FAF v4.1 = 0.143%
- All frequencies well below 1% BA1 threshold
Sources
BS1 BS1 requires allele frequency greater than expected for disorder (>0.3% by non-VCEP threshold). The highest observed population frequency is 0.237% in the Middle Eastern subpopulation (gnomAD v4.1), which approaches but does not exceed the 0.3% threshold. The overall AF across all populations is 0.012–0.017%. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1 Middle Eastern AF = 0.237% (approaches but does not cross 0.3% BS1 threshold)
- Overall AF = 0.012% (v4.1)
- 0.017% (v2.1)
- grpmax FAF v4.1 = 0.143%
Sources
Not assessed · 7 · no assessment recorded
PS3 No well-established in vitro or in vivo functional studies are available for NM_007194.4:c.1095+19G>A. No publications reporting functional characterization of this variant were identified. Details ▾Hide ▴
Evidence considered
- No functional studies identified for this specific variant
Still missing
- No functional characterization of splicing impact beyond SpliceAI prediction
PP1 No cosegregation data are available for NM_007194.4:c.1095+19G>A. No family studies or linkage data have been reported. Details ▾Hide ▴
Still missing
- No segregation or family-based linkage studies available
PP4 No patient phenotype or family history data are available for independent assessment. This adjudication is performed without access to the proband's clinical presentation or family history. Details ▾Hide ▴
Still missing
- Proband clinical phenotype and family history not provided
BS3 No well-established in vitro or in vivo functional studies demonstrating no damaging effect are available for NM_007194.4:c.1095+19G>A. While SpliceAI predicts no splice impact (computational, not functional), no experimental studies such as minigene splicing assays or RT-PCR have been performed for this variant. Details ▾Hide ▴
Evidence considered
- No experimental functional studies identified
Still missing
- Minigene splicing assay or RT-PCR data would clarify functional impact
BS4 No segregation data are available to assess lack of cosegregation with disease in affected family members. Details ▾Hide ▴
Still missing
- No family-based segregation studies available
BP2 No phasing data are available to assess whether this variant has been observed in trans with a pathogenic CHEK2 variant. Details ▾Hide ▴
Still missing
- No cis/trans phasing data available
BP5 No data are available indicating an alternate molecular basis for disease in a case carrying this variant. Details ▾Hide ▴
Still missing
- No alternate molecular diagnosis data available
Not applicable · 10· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANM_007194.4:c.1095+19G>A is an intronic variant located 19 bases downstream of exon 10, outside the canonical ±1,2 splice donor/acceptor consensus. It does not fall into the null-variant buckets of nonsense, frameshift, or canonical splice consensus required for PVS1 application. The generic PVS1 decision framework confirms apply_generic_pvs1_framework=false. Details ▾Hide ▴
Evidence considered
- Intronic variant at +19 position
- not a predicted null variant
- PVS1 variant assessment framework explicitly excludes this variant class
Sources
pvs1_variant_assessmentpvs1_gene_context
PS1 N/APS1 requires a different nucleotide change at the same position that has been established as pathogenic. No known pathogenic variant exists at the c.1095+19 position in CHEK2. Details ▾Hide ▴
Evidence considered
- No pathogenic comparator variant at the same nucleotide position
PM3 N/APM3 applies to recessive disorders where the variant is detected in trans with a pathogenic variant. CHEK2-related cancer predisposition is autosomal dominant; PM3 is not applicable. Details ▾Hide ▴
No further detail was recorded.
PM4 N/APM4 applies to protein length changes from non-frameshift indels, stop-loss, or initiation codon variants. NM_007194.4:c.1095+19G>A is a single nucleotide intronic substitution, not a protein-length altering change. Details ▾Hide ▴
No further detail was recorded.
PM5 N/APM5 applies to novel missense variants occurring at the same amino acid residue as a known pathogenic missense variant. NM_007194.4:c.1095+19G>A is an intronic variant with no protein consequence (NP_009125.1:p.?); no amino acid residue can be assigned, making PM5 inapplicable. Details ▾Hide ▴
Evidence considered
- Intronic variant with no protein consequence
- pm5_candidates.json confirms no same-residue comparator possible
PP2 N/APP2 applies to missense variants in genes with a low rate of benign missense variation where missense variants are a common disease mechanism. NM_007194.4:c.1095+19G>A is an intronic variant, not a missense change. Details ▾Hide ▴
Evidence considered
- Variant is intronic
- not missense — PP2 is not applicable
BP1 N/ABP1 applies to missense variants in genes where primarily truncating variants cause disease. NM_007194.4:c.1095+19G>A is an intronic variant, not a missense change. Details ▾Hide ▴
Evidence considered
- Variant is intronic
- not missense — BP1 is not applicable
BP3 N/ABP3 applies to in-frame deletions/insertions in repetitive regions. NM_007194.4:c.1095+19G>A is a single nucleotide intronic substitution, not an in-frame indel. Details ▾Hide ▴
No further detail was recorded.
BP7 N/ABP7 is defined for synonymous (silent) variants for which splicing prediction algorithms predict no impact and the nucleotide is not highly conserved. NM_007194.4:c.1095+19G>A is an intronic variant, not a synonymous coding change. BP7 does not apply. Details ▾Hide ▴
Evidence considered
- Variant is intronic
- not synonymous — BP7 is not applicable
PS5 N/APS5 is not a criterion in the generic ACMG/AMP 2015 framework (PMID:25741868). The standard pathogenic criteria extend from PVS1 through PP5. No gene-specific VCEP/CSPEC framework defines a PS5 criterion for CHEK2. Details ▾Hide ▴
Evidence considered
- PS5 is not defined in the applicable ACMG/AMP framework
Identifiers
- Gene
- CHEK2
- Transcript
- NM_007194.4
- Coding (HGVS c.)
- NM_007194.4:c.1095+19G>A
- Protein (HGVS p.)
- NP_009125.1:p.?
- GRCh38
- chr22:28696882 C>T
- GRCh37
- chr22:29092870 C>T
- ClinVar
- 371849
Gene diagram
Every interpreted variant in CHEK2, mapped onto the exon structure of NM_007194.4. Select a row to find it on the plot.
CHEK2NM_007194.4
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 CHEK2
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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
186 / 1,542,484 alleles
AF 0.000121 · 1 homozygotes · FAF 0.00143
gnomAD v2.1
47 / 282,086 alleles
AF 0.000167 · 0 homozygotes · FAF 0.000678
gnomAD-Canada v1.0
Allele count data not recorded
By genetic ancestry
gnomAD v4.1
AF 0.00012 · 186 / 1,542,484 alleles · 1 hom · FAF 0.0014
| Middle Eastern14 / 5,910 | 0.0024 |
| South Asian81 / 89,542 | 0.00091 hom |
| Remaining individuals10 / 60,092 | 0.00017 |
| African/African American7 / 73,590 | 9.5e-05 |
| European (non-Finnish)72 / 1,115,072 | 6.5e-05 |
| Admixed American2 / 59,900 | 3.3e-05 |
0 alternate alleles recorded in 4 other groups: European (Finnish), Amish, East Asian, Ashkenazi Jewish.
gnomAD v2.1
AF 0.00017 · 47 / 282,086 alleles · 0 hom · FAF 0.00068
| South Asian29 / 30,582 | 0.00095 |
| Remaining individuals3 / 7,190 | 0.00042 |
| African/African American4 / 24,906 | 0.00016 |
| European (non-Finnish)9 / 128,796 | 7e-05 |
| Admixed American2 / 35,374 | 5.7e-05 |
0 alternate alleles recorded in 3 other groups: Ashkenazi Jewish, East Asian, European (Finnish).
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 0.000120585; MAF= 0.01206%, 186/1542484 alleles, homozygotes = 1) and has highest observed frequency in the Middle Eastern population (AF= 0.00236887; MAF= 0.23689%, 14/5910 alleles, homozygotes = 0); grpmax FAF= 0.0014315.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.000166616; MAF= 0.01666%, 47/282086 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.00094827; MAF= 0.09483%, 29/30582 alleles, homozygotes = 0); grpmax FAF= 0.00067758.
gnomAD-Canada
Not available in gnomAD-Canada v1.0.
SpliceAI and Pangolin
Other predictors
- REVEL
- Not available
- BayesDel
- Not available
How the predictions were used
BP4 SupportingComputational evidence suggests no impact on splicing. SpliceAI predicts no splice alteration with a maximum delta score of 0.00 across all categories (acceptor gain, acceptor loss, donor gain, donor loss). The variant resides at position +19 in intron 10, well outside the canonical splice consensus, consistent with a neutral intronic change. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.00 (all categories: donor loss=0.00
- donor gain=0.00
- acceptor loss=0.00
- acceptor gain=0.00)
- Deep intronic position (+19) outside conserved splice region
Sources
PP3 Multiple lines of computational evidence do not support a deleterious effect. SpliceAI predicts no splice impact (max delta score = 0.00 for all categories: acceptor gain, acceptor loss, donor gain, donor loss). REVEL and BayesDel scores are not available for this intronic variant as they require missense changes. No in silico tool predicts pathogenicity. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.00 — no predicted splice alteration
- REVEL: not applicable (intronic variant)
- BayesDel: not applicable (intronic variant)
- HCI prior: not applicable (gene not supported)
Sources
BP7 N/ABP7 is defined for synonymous (silent) variants for which splicing prediction algorithms predict no impact and the nucleotide is not highly conserved. NM_007194.4:c.1095+19G>A is an intronic variant, not a synonymous coding change. BP7 does not apply. Details ▾Hide ▴
Evidence considered
- Variant is intronic
- not synonymous — BP7 is not applicable
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
7 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
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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.This is the ACMG/AMP 2015 standards and guidelines for interpretation of sequence variants. The paper defines the generic ACMG/AMP criteria framework but does not discuss any specific CHEK2 variant. NM_007194.4:c.1095+19G>A was not identified in this publication.Does not name this variant
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PMID 26389210 ↗Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version.PDQ Cancer Genetics Editorial Board · 2002PDQ cancer genetics summary on Genetics of Breast and Gynecologic Cancers. This is a general reference providing background on hereditary cancer syndromes. NM_007194.4:c.1095+19G>A was not identified in this publication.Does not name this variant
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PMID 26389258 ↗Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version.PDQ Cancer Genetics Editorial Board · 2002PDQ cancer genetics summary on Cancer Genetics Risk Assessment and Counseling. This is a general reference on genetic counseling practices. NM_007194.4:c.1095+19G>A was not identified in this publication.Does not name this variant
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PMID 31429903 ↗Risk Assessment, Genetic Counseling, and Genetic Testing for BRCA-Related Cancer: US Preventive Services Task Force Recommendation Statement.USPSTF Recommendation Statement on risk assessment, genetic counseling, and genetic testing for BRCA-related cancer. This paper focuses exclusively on BRCA1/2 and does not discuss CHEK2 or any CHEK2 variant. NM_007194.4:c.1095+19G>A was not identified in this publication.Does not name this variant
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PMID 35802134 ↗ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG).ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome sequencing. This policy statement lists genes recommended for secondary findings reporting but does not discuss specific variants. NM_007194.4:c.1095+19G>A was not identified in this publication.Does not name this variant
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PMID 40440438 ↗CHEK2-Related Cancer Predisposition.Adam MP et al. · 1993CHEK2-Related Cancer Predisposition (GeneReviews). This is a general clinical summary of CHEK2-associated cancer risks and management. NM_007194.4:c.1095+19G>A was not identified in the available material.Does not name this variant
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PMID 28492532 ↗Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. This paper describes a variant classification framework but does not discuss specific CHEK2 variants. NM_007194.4:c.1095+19G>A was not identified in this publication.Does not name this variant
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
186 / 1,542,484 recorded alleles
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.000
Open source ↗
ClinVar
9 Likely benign · 3 Benign
Open source ↗
COSMIC
Captured COSMIC 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/522546466
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/371849/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/22-29092870-C-T?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr22-28696882-C-T?dataset=gn…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/22-28696882-C-T
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_007194.4%3Ac.1095…
- OncoKB ↗www.oncokb.org/gene/CHEK2/?
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=CHEK2+c.1095+19G%3EA
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= 0.000120585; MAF= 0.01206%, 186/1542484 alleles, homozygotes = 1) and has highest observed frequency in the Middle Eastern population (AF= 0.00236887; MAF= 0.23689%, 14/5910 alleles, homozygotes = 0); grpmax FAF= 0.0014315.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.000166616; MAF= 0.01666%, 47/282086 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.00094827; MAF= 0.09483%, 29/30582 alleles, homozygotes = 0); grpmax FAF= 0.00067758.
gnomAD-Canada
Not available in gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Likely benign (9 clinical laboratories) and as Benign (3 clinical laboratories). (ClinVarID = 371849)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Somatic
This variant has not previously been reported in somatic cancers (COSMIC).