rs587780768
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_002354.3(EPCAM):c.496C>A(p.Leu166Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000187 in 1,604,752 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002354.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EPCAM | NM_002354.3 | c.496C>A | p.Leu166Ile | missense_variant | 5/9 | ENST00000263735.9 | NP_002345.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPCAM | ENST00000263735.9 | c.496C>A | p.Leu166Ile | missense_variant | 5/9 | 1 | NM_002354.3 | ENSP00000263735.4 | ||
EPCAM | ENST00000405271.5 | c.580C>A | p.Leu194Ile | missense_variant | 6/10 | 5 | ENSP00000385476.1 | |||
EPCAM | ENST00000456133.5 | n.580C>A | non_coding_transcript_exon_variant | 6/11 | 5 | ENSP00000410675.1 | ||||
EPCAM | ENST00000490733.1 | n.345C>A | non_coding_transcript_exon_variant | 3/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151990Hom.: 0 Cov.: 31
GnomAD4 exome AF: 6.88e-7 AC: 1AN: 1452762Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 723436
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151990Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74228
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at