rs9929218
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004360.5(CDH1):c.164-14627G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,086 control chromosomes in the GnomAD database, including 6,233 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.28 ( 6233 hom., cov: 32)
Consequence
CDH1
NM_004360.5 intron
NM_004360.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.560
Genes affected
CDH1 (HGNC:1748): (cadherin 1) This gene encodes a classical cadherin of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature glycoprotein. This calcium-dependent cell-cell adhesion protein is comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Mutations in this gene are correlated with gastric, breast, colorectal, thyroid and ovarian cancer. Loss of function of this gene is thought to contribute to cancer progression by increasing proliferation, invasion, and/or metastasis. The ectodomain of this protein mediates bacterial adhesion to mammalian cells and the cytoplasmic domain is required for internalization. This gene is present in a gene cluster with other members of the cadherin family on chromosome 16. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 16-68787043-G-A is Benign according to our data. Variant chr16-68787043-G-A is described in ClinVar as [Benign]. Clinvar id is 1623458.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-68787043-G-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH1 | NM_004360.5 | c.164-14627G>A | intron_variant | Intron 2 of 15 | ENST00000261769.10 | NP_004351.1 | ||
CDH1 | NM_001317184.2 | c.164-14627G>A | intron_variant | Intron 2 of 14 | NP_001304113.1 | |||
CDH1 | NM_001317185.2 | c.-1452-14627G>A | intron_variant | Intron 2 of 15 | NP_001304114.1 | |||
CDH1 | NM_001317186.2 | c.-1656-14627G>A | intron_variant | Intron 2 of 14 | NP_001304115.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.284 AC: 43088AN: 151968Hom.: 6233 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
43088
AN:
151968
Hom.:
Cov.:
32
Gnomad AFR
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.283 AC: 43112AN: 152086Hom.: 6233 Cov.: 32 AF XY: 0.282 AC XY: 20940AN XY: 74350 show subpopulations
GnomAD4 genome
AF:
AC:
43112
AN:
152086
Hom.:
Cov.:
32
AF XY:
AC XY:
20940
AN XY:
74350
Gnomad4 AFR
AF:
AC:
0.295684
AN:
0.295684
Gnomad4 AMR
AF:
AC:
0.253372
AN:
0.253372
Gnomad4 ASJ
AF:
AC:
0.395737
AN:
0.395737
Gnomad4 EAS
AF:
AC:
0.208076
AN:
0.208076
Gnomad4 SAS
AF:
AC:
0.256538
AN:
0.256538
Gnomad4 FIN
AF:
AC:
0.240337
AN:
0.240337
Gnomad4 NFE
AF:
AC:
0.290471
AN:
0.290471
Gnomad4 OTH
AF:
AC:
0.29281
AN:
0.29281
Heterozygous variant carriers
0
1625
3250
4876
6501
8126
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
442
884
1326
1768
2210
<30
30-35
35-40
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>80
Age
Alfa
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Bravo
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Asia WGS
AF:
AC:
982
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hereditary diffuse gastric adenocarcinoma Benign:1
Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at