rs4952886
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002354.3(EPCAM):c.859-149A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0919 in 674,418 control chromosomes in the GnomAD database, including 3,317 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.10 ( 919 hom., cov: 33)
Exomes 𝑓: 0.089 ( 2398 hom. )
Consequence
EPCAM
NM_002354.3 intron
NM_002354.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.242
Genes affected
EPCAM (HGNC:11529): (epithelial cell adhesion molecule) This gene encodes a carcinoma-associated antigen and is a member of a family that includes at least two type I membrane proteins. This antigen is expressed on most normal epithelial cells and gastrointestinal carcinomas and functions as a homotypic calcium-independent cell adhesion molecule. The antigen is being used as a target for immunotherapy treatment of human carcinomas. Mutations in this gene result in congenital tufting enteropathy. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 2-47385017-A-G is Benign according to our data. Variant chr2-47385017-A-G is described in ClinVar as [Benign]. Clinvar id is 1244355.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPCAM | NM_002354.3 | c.859-149A>G | intron_variant | ENST00000263735.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPCAM | ENST00000263735.9 | c.859-149A>G | intron_variant | 1 | NM_002354.3 | P1 | |||
EPCAM | ENST00000405271.5 | c.943-149A>G | intron_variant | 5 | |||||
EPCAM | ENST00000456133.5 | c.943-149A>G | intron_variant, NMD_transcript_variant | 5 | |||||
EPCAM | ENST00000490733.1 | n.708-149A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.103 AC: 15672AN: 152088Hom.: 917 Cov.: 33
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GnomAD4 exome AF: 0.0886 AC: 46271AN: 522212Hom.: 2398 AF XY: 0.0874 AC XY: 24704AN XY: 282742
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GnomAD4 genome ? AF: 0.103 AC: 15683AN: 152206Hom.: 919 Cov.: 33 AF XY: 0.105 AC XY: 7850AN XY: 74428
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 06, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at