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]
Link to SEPIO compliant JSON-LD document
  • No ClinVar Id was directly found from the curated document
  • ClinVar Id was derived from the Allele Registry.

Variant: NM_004360.3:c.1137G>T

CA496153150

599655 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: e4b2700f-9760-4cfc-8513-12d276db2589

HGVS expressions

NM_004360.3:c.1137G>T
NC_000016.10:g.68812263G>T
CM000678.2:g.68812263G>T
NC_000016.9:g.68846166G>T
CM000678.1:g.68846166G>T
NC_000016.8:g.67403667G>T
NG_008021.1:g.79972G>T
ENST00000261769.10:c.1137G>T
ENST00000261769.9:c.1137G>T
ENST00000422392.6:c.1137G>T
ENST00000562836.5:n.1208G>T
ENST00000565810.1:n.181G>T
ENST00000566510.5:c.981G>T
ENST00000566612.5:c.1137G>T
ENST00000611625.4:c.1137G>T
ENST00000612417.4:c.1137G>T
ENST00000621016.4:c.1137G>T
NM_001317184.1:c.1137G>T
NM_001317185.1:c.-479G>T
NM_001317186.1:c.-683G>T
NM_004360.4:c.1137G>T
NM_004360.5:c.1137G>T
NM_001317184.2:c.1137G>T
NM_001317185.2:c.-479G>T
NM_001317186.2:c.-683G>T
NM_004360.5(CDH1):c.1137G>T (p.Thr379=)

Likely Pathogenic

Met criteria codes 4
PP3_Moderate PM2_Supporting PS4_Supporting PVS1_Moderate
Not Met criteria codes 22
PM6 PM3 PM1 PM4 PM5 BA1 BS2 BS4 BS3 BS1 BP2 BP3 BP1 BP4 BP5 BP7 PS2 PS3 PS1 PP4 PP1 PP2

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 c.1137G>T p. (Thr379=) variant results in a G to non-G change at the last nucleotide of an exon (PVS1_Moderate). The variant is absent in the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). This variant affects the same splice site as a well-characterized splice variant with similar or worse in silico/ RNA predictions (PP3_Moderate). Additionally, this variant has been reported in at least one family meeting HDGC clinical criteria (PS4_Supporting; PMID: 26182300). 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_Moderate, PM2_Supporting, PP3_Moderate, PS4_Supporting.
Met criteria codes
PP3_Moderate
This variant affects the same splice site as a well-characterized splice variant with similar or worse in silico/ RNA predictions
PM2_Supporting
The variant is absent in the gnomAD cohort
PS4_Supporting
This variant has been reported in at least one family meeting HDGC clinical criteria
PVS1_Moderate
The c.1137G>T p. (Thr379=) variant results in a G to non-G change at the last nucleotide of an exon
Not Met criteria codes
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
Not at a canonical splicing site.
BA1
The variant is absent in the gnomAD cohort
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
The variant is absent in the gnomAD cohort
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
This variant affects the same splice site as a well-characterized splice variant with similar or worse in silico/ RNA predictions
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-08-30
Published on: 2023-08-30
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