chr2-47375266-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_002354.3(EPCAM):āc.458G>Cā(p.Arg153Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00023 in 1,612,484 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R153G) has been classified as Uncertain significance.
Frequency
Consequence
NM_002354.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPCAM | NM_002354.3 | c.458G>C | p.Arg153Thr | missense_variant | 4/9 | ENST00000263735.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPCAM | ENST00000263735.9 | c.458G>C | p.Arg153Thr | missense_variant | 4/9 | 1 | NM_002354.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000724 AC: 182AN: 251266Hom.: 0 AF XY: 0.000685 AC XY: 93AN XY: 135826
GnomAD4 exome AF: 0.000220 AC: 321AN: 1460224Hom.: 1 Cov.: 29 AF XY: 0.000227 AC XY: 165AN XY: 726504
GnomAD4 genome AF: 0.000328 AC: 50AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.000443 AC XY: 33AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | EPCAM: BP4 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 02, 2021 | - - |
Lynch syndrome 1 Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Ding PR Lab, Sun Yat-sen University Cancer Center | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 24, 2016 | - - |
EPCAM-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 09, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at