rs750826481
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PP3_Strong
The NM_002354.3(EPCAM):c.643T>A(p.Tyr215Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000241 in 1,577,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y215S) has been classified as Uncertain significance.
Frequency
Consequence
NM_002354.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPCAM | NM_002354.3 | c.643T>A | p.Tyr215Asn | missense_variant | 6/9 | ENST00000263735.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPCAM | ENST00000263735.9 | c.643T>A | p.Tyr215Asn | missense_variant | 6/9 | 1 | NM_002354.3 | P1 | |
EPCAM | ENST00000405271.5 | c.727T>A | p.Tyr243Asn | missense_variant | 7/10 | 5 | |||
EPCAM | ENST00000490733.1 | n.492T>A | non_coding_transcript_exon_variant | 4/6 | 3 | ||||
EPCAM | ENST00000456133.5 | c.727T>A | p.Tyr243Asn | missense_variant, NMD_transcript_variant | 7/11 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251218Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135806
GnomAD4 exome AF: 0.0000253 AC: 36AN: 1424884Hom.: 0 Cov.: 25 AF XY: 0.0000239 AC XY: 17AN XY: 711138
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
Hereditary nonpolyposis colorectal neoplasms Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 07, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at