rs281865545
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_000442.5(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
Genomes: š 0.46 ( 16619 hom., cov: 30)
Exomes š: 0.49 ( 38533 hom. )
Consequence
PECAM1
NM_000442.5 missense
NM_000442.5 missense
Scores
6
Clinical Significance
Conservation
PhyloP100: -0.159
Genes affected
PECAM1 (HGNC:8823): (platelet and endothelial cell adhesion molecule 1) The protein encoded by this gene is found on the surface of platelets, monocytes, neutrophils, and some types of T-cells, and makes up a large portion of endothelial cell intercellular junctions. The encoded protein is a member of the immunoglobulin superfamily and is likely involved in leukocyte migration, angiogenesis, and integrin activation. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0066434443).
BP6
?
Variant 17-64377836-C-G is Benign according to our data. Variant chr17-64377836-C-G is described in ClinVar as [Benign]. Clinvar id is 156304.Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PECAM1 | NM_000442.5 | c.373G>C | p.Val125Leu | missense_variant | 3/16 | ENST00000563924.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PECAM1 | ENST00000563924.6 | c.373G>C | p.Val125Leu | missense_variant | 3/16 | 1 | NM_000442.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.465 AC: 70500AN: 151672Hom.: 16601 Cov.: 30
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GnomAD4 exome AF: 0.485 AC: 156723AN: 323062Hom.: 38533 Cov.: 0 AF XY: 0.487 AC XY: 82009AN XY: 168560
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GnomAD4 genome ? AF: 0.465 AC: 70564AN: 151788Hom.: 16619 Cov.: 30 AF XY: 0.469 AC XY: 34815AN XY: 74154
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ClinVar
Significance: Benign
Submissions summary: Benign:2Other:1
Revision: no assertion criteria provided
LINK: link
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
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
CADD
Benign
LIST_S2
Benign
T;T;T;T
MetaRNN
Benign
T;T;T;T
PROVEAN
Benign
N;N;N;N
Sift
Benign
T;T;T;T
Sift4G
Benign
T;.;.;.
Vest4
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at