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

Variant: NM_004360.4(CDH1):c.457_460delAAGA (p.Lys153Glufs)

CA658683946

491538 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 803b9285-eb66-46d9-9b50-0894c44a93be
Approved on: 2023-08-04
Published on: 2023-08-04

HGVS expressions

NM_004360.4:c.457_460delAAGA
NM_004360.4(CDH1):c.457_460delAAGA (p.Lys153Glufs)
NC_000016.10:g.68808493_68808496del
CM000678.2:g.68808493_68808496del
NC_000016.9:g.68842396_68842399del
CM000678.1:g.68842396_68842399del
NC_000016.8:g.67399897_67399900del
NG_008021.1:g.76202_76205del
ENST00000261769.10:c.457_460del
ENST00000261769.9:c.457_460del
ENST00000422392.6:c.457_460del
ENST00000561751.1:c.224_227del
ENST00000562836.5:n.528_531del
ENST00000564676.5:n.739_742del
ENST00000564745.1:n.452_455del
ENST00000566510.5:c.457_460del
ENST00000566612.5:c.457_460del
ENST00000611625.4:c.457_460del
ENST00000612417.4:c.457_460del
ENST00000621016.4:c.457_460del
NM_004360.3:c.457_460del
NM_001317184.1:c.457_460del
NM_001317185.1:c.-1159_-1156del
NM_001317186.1:c.-1363_-1360del
NM_004360.4:c.457_460del
NM_004360.5:c.457_460del
NM_001317184.2:c.457_460del
NM_001317185.2:c.-1159_-1156del
NM_001317186.2:c.-1363_-1360del
NM_004360.5(CDH1):c.457_460del (p.Lys153fs)

Pathogenic

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

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.457_460del (p.Lys153Glufs*61) 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
PM2_Supporting
Absent in gnomAD cohort.
PVS1
Deletion of 4 bp in exon 4 of 16, predicted to result in NMD.
PM5_Supporting
Deletion of 4 bp in exon 4 of 16, predicted to result in NMD.
Not Met criteria codes
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
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
BP4
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
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
PS4
Proband with pathology unknown (SCV000689540.1). This does not meet HDGC clinical criteria.
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
PP3
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
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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