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CDH1
Final classification
Likely Benign
CDH1 c.2053G>A · p.Val685Met
CDH1

NM_004360.5:c.2053G>A (p.Val685Met) is a missense variant in CDH1 exon 13. The ClinGen CDH1 Expert Panel has classified this variant as Likely benign (ClinVar Variation ID: 133847).

Gene
CDH1
Transcript
NM_004360.5
HGVS · transcript:coding
NM_004360.5:c.2053G>A
Consequence
N/A
GRCh38
chr16:68823515 G>A
GRCh37
chr16:68857418 G>A
Basis ClinGen CDH1 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 3.1 v3.1.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BP2 supporting benign, BP6 supporting benign; combination = 2 supporting benign, which maps to Likely Benign.
ClinGen CDH1 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 3.1 v3.1.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BP2 supporting benign, BP6 supporting benign; combination = 2 supporting benign, which maps to Likely Benign.
Classification rationale
BP2BP6 Likely Benign
CDH1 c.2053G>A

NM_004360.5:c.2053G>A (p.Val685Met) is a missense variant in CDH1 exon 13. The ClinGen CDH1 Expert Panel has classified this variant as Likely benign (ClinVar Variation ID: 133847).1 The variant is present in gnomAD population databases at low frequency: 4/251,468 alleles in v2.1 (AF 0.00159%) and 24/1,613,720 alleles in v4.1 (AF 0.00149%), with one homozygote reported in v4.1. These frequencies exceed the CDH1 VCEP PM2 threshold of ≤1/100,000 alleles, and the homozygote observation meets BP2_Supporting under the VCEP rules.2 SpliceAI predicts no significant splicing impact (max delta score 0.11). In silico protein predictors show borderline scores (REVEL 0.47; BayesDel -0.1394), but per CDH1 VCEP, protein-based computational models are not used for PP3/BP4 assessment.3 No variant-specific functional studies, segregation data, de novo reports, or case-control studies were identified in the reviewed literature. Six full-text papers and 10 additional abstracts were reviewed; none mention NM_004360.5:c.2053G>A or p.Val685Met. One homozygote in gnomAD v4.1 meets CDH1 VCEP BP2_Supporting ('observed in the homozygous state in gnomAD'), providing a single line of benign evidence. No other ACMG criteria are met with the available evidence. Most criteria remain unassessed due to lack of variant-specific functional, segregation, or clinical phenotype data.4

BP2 + BP6 Likely Benign
Gene diagram · NM_004360.5 · variants mapped to exon structure
CDH1 NM_004360.5
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports benign
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 1.48725e-05; MAF= 0.00149%, 24/1613720 alleles, homozygotes = 1) and has highest observed frequency in the Admixed American population (AF= 0.000133333; MAF= 0.01333%, 8/60000 alleles, homozygotes = 0); grpmax FAF= 6.615e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.59066e-05; MAF= 0.00159%, 4/251468 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 6.15157e-05; MAF= 0.00615%, 1/16256 alleles, homozygotes = 0); grpmax FAF= 9.58e-06.
      🇨🇦 CA
      This variant is present in gnomAD-Canada v1.0 (AF= 0.00010856584518510477, 2/18422 alleles, homozygotes = 0).
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0015% · 24 / 1,613,720
      1 hom · FAF 0.0066%
      Admixed American
      8 / 60,000
      0.013%
      East Asian
      2 / 44,886
      0.0045%
      African/African American
      3 / 75,016
      0.004%
      1 hom
      South Asian
      2 / 91,070
      0.0022%
      Remaining individuals
      1 / 62,494
      0.0016%
      European (non-Finnish)
      8 / 1,179,670
      0.00068%
      + 4 not observed (European (Finnish), Amish, Middle Eastern, Ashkenazi Jewish)
      gnomAD v2.1
      0.0016% · 4 / 251,468
      0 hom · FAF 0.00096%
      African/African American
      1 / 16,256
      0.0062%
      Admixed American
      2 / 34,592
      0.0058%
      East Asian
      1 / 18,394
      0.0054%
      + 5 not observed (Ashkenazi Jewish, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      0.011% · 2 / 18,422
      0 hom · FAF 0.042%
      Latino/Admixed American
      2 / 838
      0.24%
      + 8 not observed (African/African American, Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, European (non-Finnish), Remaining individuals, South Asian)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (5 clinical laboratories) and as Uncertain significance (2 clinical laboratories) and as Likely benign by Clingen Gastric Cancer Variant Curation Expert Panel (expert panel). (ClinVarID = 133847)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.11). REVEL score = 0.47. BayesDel score = -0.1394.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. CDH1 (E-cadherin), a tumor suppressor involved in cell adhesion, is altered by mutation or deletion in various cancer typess, most frequently in breas
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV55733838, n = 1 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 PMIDs not cited in assessment
      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. CLINVAR
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      29936259 ↗ Analytical Validation of a Hybrid Capture-Based Next-Generation Sequencing Clinical Assay for Genomic Profiling of Cell-Free Circulating Tumor DNA. CLINVAR
      31925297 ↗ Diversity spectrum analysis identifies mutation-specific effects of cancer driver genes. CLINVAR
      17392385 ↗ American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. CLINVAR
      20065170 ↗ American Society of Clinical Oncology policy statement update: genetic and genomic testing for cancer susceptibility. CLINVAR
      24728327 ↗ Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. CLINVAR
      26324357 ↗ American Society of Clinical Oncology Policy Statement Update: Genetic and Genomic Testing for Cancer Susceptibility. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR