rs371372017
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_002354.3(EPCAM):c.516G>A(p.Thr172=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,610,992 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 (★★). Synonymous variant affecting the same amino acid position (i.e. T172T) has been classified as Likely benign.
Frequency
Consequence
NM_002354.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPCAM | NM_002354.3 | c.516G>A | p.Thr172= | synonymous_variant | 5/9 | ENST00000263735.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPCAM | ENST00000263735.9 | c.516G>A | p.Thr172= | synonymous_variant | 5/9 | 1 | NM_002354.3 | P1 | |
EPCAM | ENST00000405271.5 | c.600G>A | p.Thr200= | synonymous_variant | 6/10 | 5 | |||
EPCAM | ENST00000490733.1 | n.365G>A | non_coding_transcript_exon_variant | 3/6 | 3 | ||||
EPCAM | ENST00000456133.5 | c.600G>A | p.Thr200= | synonymous_variant, NMD_transcript_variant | 6/11 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151994Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251374Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135874
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1458998Hom.: 0 Cov.: 28 AF XY: 0.0000220 AC XY: 16AN XY: 726044
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151994Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74230
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 30, 2015 | - - |
EPCAM-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 22, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 21, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at