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.79C>T (p.Pro27Ser)

CA10583401

239913 (ClinVar)

Gene: CDH1
Condition: CDH1-related diffuse gastric and lobular breast cancer
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 9a9082a0-343e-4b16-a256-c64b923d37b2

HGVS expressions

NM_004360.4:c.79C>T
NM_004360.4(CDH1):c.79C>T (p.Pro27Ser)
NC_000016.10:g.68738327C>T
CM000678.2:g.68738327C>T
NC_000016.9:g.68772230C>T
CM000678.1:g.68772230C>T
NC_000016.8:g.67329731C>T
NG_008021.1:g.6036C>T
ENST00000261769.10:c.79C>T
ENST00000261769.9:c.79C>T
ENST00000422392.6:c.79C>T
ENST00000566510.5:c.79C>T
ENST00000566612.5:c.79C>T
ENST00000611625.4:c.79C>T
ENST00000612417.4:c.79C>T
ENST00000621016.4:c.79C>T
NM_004360.3:c.79C>T
NM_001317184.1:c.79C>T
NM_001317185.1:c.-1537C>T
NM_001317186.1:c.-1741C>T
NM_004360.5:c.79C>T
NM_001317184.2:c.79C>T
NM_001317185.2:c.-1537C>T
NM_001317186.2:c.-1741C>T
NM_004360.5(CDH1):c.79C>T (p.Pro27Ser)

Uncertain Significance

Met criteria codes 1
PM2_Supporting
Not Met criteria codes 25
PS2 PS4 PS3 PS1 BP5 BP7 BP2 BP3 BP1 BP4 PVS1 BA1 PP1 PP4 PP2 PP3 PM3 PM1 PM4 PM5 PM6 BS4 BS3 BS1 BS2

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.79C>T (p.Pro27Ser) variant has allele frequency <1 out of 100, 000 in the gnomAD cohort (1/156646 in gnomAD v2.1.1; PM2_Supporting). No additional evidence met criteria for consideration. In summary, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): PM2_Supporting.
Met criteria codes
PM2_Supporting
Allele frequency <1 out of 100, 000 (1/156646 in gnomAD v2.1.1).
Not Met criteria codes
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
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
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
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
REVEL, SIFT, PolyPhen2-HVAR, MutationTaster, MutationAssessor, FATHMM, PROVEAN, MetaSVM, and CADD predict benign. P27S observed in Marmoset, Rat, and Mouse. No new splice site predicted by NNSPLICE, however HumanSplicingFinder predicts: "Alteration of an exonic ESE site. Potential alteration of splicing."
PVS1
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
PP1
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
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL, SIFT, PolyPhen2-HVAR, MutationTaster, MutationAssessor, FATHMM, PROVEAN, MetaSVM, and CADD predict benign. P27S observed in Marmoset, Rat, and Mouse. No new splice site predicted by NNSPLICE, however HumanSplicingFinder predicts: "Alteration of an exonic ESE site. Potential alteration of splicing."
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
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
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
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-08-21
Published on: 2023-08-21
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