rs376155665
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_002354.3(EPCAM):c.556-14A>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000607 in 1,153,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000010 ( 0 hom. )
Consequence
EPCAM
NM_002354.3 splice_polypyrimidine_tract, intron
NM_002354.3 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0690
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 Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 2-47378939-A-C is Benign according to our data. Variant chr2-47378939-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 1080999.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPCAM | NM_002354.3 | c.556-14A>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000263735.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPCAM | ENST00000263735.9 | c.556-14A>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002354.3 | P1 | |||
EPCAM | ENST00000405271.5 | c.640-14A>C | splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
EPCAM | ENST00000456133.5 | c.640-14A>C | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 5 | |||||
EPCAM | ENST00000490733.1 | n.405-14A>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152060Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248832Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134840
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GnomAD4 exome AF: 9.98e-7 AC: 1AN: 1001604Hom.: 0 Cov.: 14 AF XY: 0.00000193 AC XY: 1AN XY: 518722
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GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152060Hom.: 0 Cov.: 33 AF XY: 0.0000539 AC XY: 4AN XY: 74260
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at