Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with ClinVar but not with the Allele Registry data

Variant: NM_004360.5(CDH1):c.467G>A (p.Trp156Ter)

463781 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 6cb9aca3-f806-41d5-9c8e-94aa0916aee1
Approved on: 2023-08-04
Published on: 2023-08-04

HGVS expressions

NM_004360.5:c.467G>A
NM_004360.5(CDH1):c.467G>A (p.Trp156Ter)

Pathogenic

Met criteria codes 3
PM5_Supporting PM2_Supporting PVS1
Not Met criteria codes 23
BS4 BS3 BS1 BS2 BP5 BP7 BP2 BP3 BP4 BP1 PS2 PS4 PS3 PS1 BA1 PP4 PP1 PP3 PP2 PM3 PM1 PM4 PM6

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen CDH1 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 3.1

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
CDH1 VCEP
The CDH1 c.467G>A (p.Trp156Ter) variant is predicted to result in a premature stop codon that leads to nonsense mediate decay (PVS1 and PM5_supporting). The variant is absent in the gnomAD cohort (PM2_supporting; http://gnomad.broadinstitute.org). Therefore, this variant meets criteria to be classified as pathogenic based on the ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (CDH1 VCEP specifications version 3.1): PVS1, PM2_supporting, PM5_supporting.
Met criteria codes
PM5_Supporting
This variant results in a nonsense codon predicted to under NMD.
PM2_Supporting
This variant is absent from populations in gnomAD, ExAC, 1000 Genomes and ESP.
PVS1
This variant results in a nonsense codon predicted to under NMD.
Not Met criteria codes
BS4
This information is not available.
BS3
To our knowledge, no evidence supporting BS3 has been reported for this variant.
BS1
This variant is absent from populations in gnomAD, ExAC, 1000 Genomes and ESP.
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
To our knowledge, this variant has not been reported in a case with an alternate molecular basis for disease.
BP7
BP7 does not apply to nonsense variants.
BP2
To our knowledge, this variant has not been reported in cis or trans with a known pathogenic variant.
BP3
BP3 does not apply to CDH1.
BP4
BP4 does not apply to nonsense variants.
BP1
BP1 does not apply to CDH1.
PS2
This information is not available.
PS4
SCV000637830.1 and GeneDx - these families do not meet IGCLC criteria for HDGC.
PS3
PS3 does not apply to nonsense variants.
PS1
PS1 does not apply to nonsense variants.
BA1
This variant is absent from populations in gnomAD, ExAC, 1000 Genomes and ESP.
PP4
PP4 does not apply to CDH1.
PP1
This information is not available.
PP3
PP3 does not apply to nonsense variants.
PP2
PP2 does not apply to CDH1.
PM3
PM3 does not apply to CDH1.
PM1
PM1 does not apply to CDH1.
PM4
PM4 does not apply to nonsense variants.
PM6
This information is not available.
Curation History
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