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 the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_004360.5(CDH1):c.832+1G>A

CA396459027

463795 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: cc34c30c-3789-40a7-9f1b-131a3a3bfb85
Approved on: 2023-08-24
Published on: 2023-08-24

HGVS expressions

NM_004360.5:c.832+1G>A
NM_004360.5(CDH1):c.832+1G>A
NC_000016.10:g.68810342G>A
CM000678.2:g.68810342G>A
NC_000016.9:g.68844245G>A
CM000678.1:g.68844245G>A
NC_000016.8:g.67401746G>A
NG_008021.1:g.78051G>A
ENST00000261769.10:c.832+1G>A
ENST00000261769.9:c.832+1G>A
ENST00000422392.6:c.832+1G>A
ENST00000561751.1:c.455-1342G>A
ENST00000562836.5:n.903+1G>A
ENST00000566510.5:c.676+1G>A
ENST00000566612.5:c.832+1G>A
ENST00000611625.4:c.832+1G>A
ENST00000612417.4:c.832+1G>A
ENST00000621016.4:c.832+1G>A
NM_004360.3:c.832+1G>A
NM_001317184.1:c.832+1G>A
NM_001317185.1:c.-784+1G>A
NM_001317186.1:c.-988+1G>A
NM_004360.4:c.832+1G>A
NM_001317184.2:c.832+1G>A
NM_001317185.2:c.-784+1G>A
NM_001317186.2:c.-988+1G>A
More

Likely Pathogenic

Met criteria codes 4
PM5_Supporting PS4_Supporting PM2_Supporting PVS1_Strong
Not Met criteria codes 22
BS2 BS1 BS4 BS3 BP4 BP3 BP1 BP2 BP5 BP7 PS1 PS2 PS3 PM1 PM3 PM4 PM6 BA1 PP1 PP2 PP3 PP4

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.832+1G>A variant is a canonical splice variant predicted to result in a truncated or absent protein (PVS1_Strong, PM5_Supporting). The variant is absent from the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). This variant was observed in one family meeting IGCLC criteria for HDGC (PS4_Supporting, SCV000637855.2). In summary, this variant meets criteria to be classified as likely pathogenic based on the ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): PVS1_Strong, PM2_Supporting, PS4_Supporting, PM5_Supporting.
Met criteria codes
PM5_Supporting
Apply PM5_Supporting to the variant with the alteration at canonical splicing site.
PS4_Supporting
One family meets IGCLC criteria for HDGC and supports the use of PS4_Supporting (SCV000637855.2).
PM2_Supporting
This variant is absent from populations in gnomAD, ExAC, 1000 Genomes and ESP.
PVS1_Strong
This variant is at a canonical splice site, and therefore PVS1_Strong is applied.
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
This variant is absent from populations in gnomAD, ExAC, 1000 Genomes and ESP.
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
To our knowledge, no functional studies for this variant have been reported.
BP4
BP4 does not apply to canonical splice site variants.
BP3
BP3 does not apply to CDH1.
BP1
BP1 does not apply to CDH1.
BP2
To our knowledge, this variant has not been reported in cis or trans with a pathogenic variant.
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 canonical splice site variants.
PS1
PS1 does not apply to splicing variants.
PS2
This information is not available.
PS3
To our knowledge, no functional studies for this variant have been reported.
PM1
PM1 does not apply to CDH1.
PM3
To our knowledge, this variant has not been reported in cis or trans with a pathogenic variant.
PM4
PM4 does not apply to canonical splice site variants.
PM6
This information is not available.
BA1
This variant is absent from populations in gnomAD, ExAC, 1000 Genomes and ESP.
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
PP2 does not apply to CDH1.
PP3
PP3 does not apply to canonical splice site variants.
PP4
PP4 does not apply to CDH1.
Curation History
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