Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Link to SEPIO compliant JSON-LD document

Variant: NM_004360.5(CDH1):c.7C>T (p.Pro3Ser)

CA16620227

418111 (ClinVar)

Gene: CDH1

Condition: CDH1-related diffuse gastric and lobular breast cancer

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 916169ad-d424-4f36-8530-42c87c14d450

Approved on: 2023-08-21

Published on: 2023-08-21

HGVS expressions

NM_004360.5:c.7C>T

NM_004360.5(CDH1):c.7C>T (p.Pro3Ser)

NC_000016.10:g.68737422C>T

CM000678.2:g.68737422C>T

NC_000016.9:g.68771325C>T

CM000678.1:g.68771325C>T

NC_000016.8:g.67328826C>T

NG_008021.1:g.5131C>T

ENST00000261769.10:c.7C>T

ENST00000261769.9:c.7C>T

ENST00000422392.6:c.7C>T

ENST00000566510.5:c.7C>T

ENST00000566612.5:c.7C>T

ENST00000611625.4:c.7C>T

ENST00000612417.4:c.7C>T

ENST00000621016.4:c.7C>T

NM_004360.3:c.7C>T

NM_001317184.1:c.7C>T

NM_001317185.1:c.-1609C>T

NM_001317186.1:c.-1813C>T

NM_004360.4:c.7C>T

NM_001317184.2:c.7C>T

NM_001317185.2:c.-1609C>T

NM_001317186.2:c.-1813C>T

Uncertain Significance

PM2_Supporting

PP4 PP1 PP3 PP2 PM5 PM3 PM1 PM4 PS1 PS2 PS4 PS3 PM6 BA1 BP5 BP7 BP2 BP3 BP4 BP1 PVS1 BS4 BS3 BS1 BS2

Evidence Links 0

Expert Panel

CDH1 VCEP

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 c.7C>T (p.Pro3Ser) is absent from gnomAD (PM2_Supporting; http://gnomad.broadinstitute.org). In summary, the clinical significance of this variant is classified as a variant of uncertain significance based on ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): PM2 _Supporting.

PM2_Supporting

This variant is absent from populations in gnomAD, ExAC, 1000 Genomes and ESP.

PP4

PP4 does not apply to CDH1.

PP1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

PP3

This variant is not predicted to result in abnormal splicing by in silico splice site predictors.

PP2

PP2 does not apply to CDH1.

PM5

PM5 does not apply to CDH1.

PM3

PM3 does not apply to CDH1.

PM1

BP1 does not apply to CDH1.

PM4

PM4 does not apply to this variant.

PS1

No pathogenic variants resulting in the same amino acid change have been described.

PS2

To our knowledge, this variant has not been observed de novo.

PS4

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

PS3

PS3 does not apply to this variant.

PM6

To our knowledge, this variant has not been observed de novo.

BA1

This variant is absent from populations in gnomAD, ExAC, 1000 Genomes and ESP.

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 this variant.

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

This variant is not predicted to result in abnormal splicing by in silico splice site predictors.

BP1

BP1 does not apply to CDH1.

PVS1

PVS1 does not apply to this variant.

BS4

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

BS3

BS3 does not apply to this variant.

BS1

This variant is absent from populations in gnomAD, ExAC, 1000 Genomes and ESP.

BS2

This variant was observed in 2 individuals without DGC, SRC tumours or LBC and whose family history does not suggest HDGC (SCV000564833.3, SCV000957806.1).

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