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.2439+22C>T

CA8130277

259293 (ClinVar)

Gene: CDH1

Condition: CDH1-related diffuse gastric and lobular breast cancer

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: cae966bb-09fc-42e2-afa9-87358bd5f675

HGVS expressions

NM_004360.5:c.2439+22C>T

NM_004360.5(CDH1):c.2439+22C>T

NC_000016.10:g.68829819C>T

CM000678.2:g.68829819C>T

NC_000016.9:g.68863722C>T

CM000678.1:g.68863722C>T

NC_000016.8:g.67421223C>T

NG_008021.1:g.97528C>T

ENST00000261769.10:c.2439+22C>T

ENST00000261769.9:c.2439+22C>T

ENST00000422392.6:c.2256+22C>T

ENST00000562118.1:n.657+22C>T

ENST00000562836.5:n.2510+22C>T

ENST00000566510.5:c.*1105+22C>T

ENST00000566612.5:c.*679+22C>T

ENST00000611625.4:c.2502+22C>T

ENST00000612417.4:c.1853+3265C>T

ENST00000621016.4:c.1866-4384C>T

NM_004360.3:c.2439+22C>T

NM_001317184.1:c.2256+22C>T

NM_001317185.1:c.891+22C>T

NM_001317186.1:c.474+22C>T

NM_004360.4:c.2439+22C>T

NM_001317184.2:c.2256+22C>T

NM_001317185.2:c.891+22C>T

NM_001317186.2:c.474+22C>T

Benign

BA1

PVS1 BS4 BS3 BS1 BS2 BP5 BP7 BP2 BP3 BP4 BP1 PS2 PS4 PS3 PS1 PP4 PP1 PP3 PP2 PM6 PM2 PM3 PM1 PM4 PM5

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.2439+22C>T has a frequency of 0.00096 in gnomAD (271 of 280,840), with a maximum subpopulation frequency of 0.01029 (255 of 24,778) in the African population and includes one homozygote (BA1; http://gnomad.broadinstitute.org). To our knowledge, this variant has not been reported in the literature. In summary, this variant meets criteria to be classified as benign based on ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BA1.

BA1

This variant has a frequency of 0.00096 in gnomAD (271 of 280,840), with a maximum subpopulation frequency of 0.01029 (255 of 24,778) in the African population, including one homozygote.

PVS1

PVS1 does not apply to this variant.

BS4

To our knowledge, this variant has not been reported in individuals meeting IGCLC criteria for HDGC.

BS3

To our knowledge, functional studies supporting an alteration in splicing have not been reported for this variant.

BS1

This variant has a frequency of 0.00096 in gnomAD (271 of 280,840), with a maximum subpopulation frequency of 0.01029 (255 of 24,778) in the African population, including one homozygote.

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 observed 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 pathogenic variant.

BP3

BP3 does not apply to CDH1.

BP4

This variant is not predicted to alter splicing by multiple in silico tools.

BP1

BP1 does not apply to CDH1.

PS2

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

PS4

To our knowledge, this variant has not been reported in individuals meeting IGCLC criteria for HDGC.

PS3

To our knowledge, functional studies supporting an alteration in splicing have not been reported for this variant.

PS1

PS1 does not apply to this variant.

PP4

PP4 does not apply to CDH1.

PP1

To our knowledge, this variant has not been reported in individuals meeting IGCLC criteria for HDGC.

PP3

This variant is not predicted to alter splicing by multiple in silico tools.

PP2

PP2 does not apply to CDH1.

PM6

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

PM2

This variant has a frequency of 0.00096 in gnomAD (271 of 280,840), with a maximum subpopulation frequency of 0.01029 (255 of 24,778) in the African population, including one homozygote.

PM3

PM3 does not apply to CDH1.

PM1

PM1 does not apply to CDH1.

PM4

PM4 does not apply to this variant.

PM5

PM5 does not apply to CDH1.

Approved on: 2023-08-08

Published on: 2023-08-08

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