rs281865545
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The ENST00000563924.6(PECAM1):āc.373G>Cā(p.Val125Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 474,850 control chromosomes in the GnomAD database, including 55,152 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/7 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
ENST00000563924.6 missense
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PECAM1 | NM_000442.5 | c.373G>C | p.Val125Leu | missense_variant | 3/16 | ENST00000563924.6 | NP_000433.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PECAM1 | ENST00000563924.6 | c.373G>C | p.Val125Leu | missense_variant | 3/16 | 1 | NM_000442.5 | ENSP00000457421 | P1 |
Frequencies
GnomAD3 genomes AF: 0.465 AC: 70500AN: 151672Hom.: 16601 Cov.: 30
GnomAD4 exome AF: 0.485 AC: 156723AN: 323062Hom.: 38533 Cov.: 0 AF XY: 0.487 AC XY: 82009AN XY: 168560
GnomAD4 genome AF: 0.465 AC: 70564AN: 151788Hom.: 16619 Cov.: 30 AF XY: 0.469 AC XY: 34815AN XY: 74154
ClinVar
Submissions by phenotype
PLATELET-ENDOTHELIAL CELL ADHESION MOLECULE 1 POLYMORPHISM Benign:1
Benign, no assertion criteria provided | literature only | OMIM | Feb 01, 1996 | - - |
Three Vessel Coronary Disease Benign:1
Benign, no assertion criteria provided | clinical testing | Department of Cardiology, Chinese Academy of Medical Sciences, Fuwai Hospital | - | - - |
not provided Other:1
not provided, no classification provided | literature only | ClinVar Staff, National Center for Biotechnology Information (NCBI) | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at