Variant rs281865545 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_000442.5(PECAM1):c.373G>C(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: 𝑓 0.46 ( 16619 hom., cov: 30)

Exomes 𝑓: 0.49 ( 38533 hom. )

Consequence

PECAM1
NM_000442.5 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:2O:1

Conservation

PhyloP100: -0.159

Variant links:

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]

PECAM1 links:

Genome browser will be placed here

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 rank	MANE	Protein	UniProt
PECAM1	NM_000442.5 link	c.373G>C	p.Val125Leu	missense_variant	Exon 3 of 16	ENST00000563924.6	NP_000433.4	P16284-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PECAM1	ENST00000563924.6 link	c.373G>C	p.Val125Leu	missense_variant	Exon 3 of 16	1	NM_000442.5	ENSP00000457421.1		P16284-1

Frequencies

GnomAD3 genomes

AF:

0.465

AC:

70500

AN:

151672

Hom.:

16601

Cov.:

show subpopulations

Gnomad AFR

AF:

0.388

Gnomad AMI

AF:

0.640

Gnomad AMR

AF:

0.532

Gnomad ASJ

AF:

0.541

Gnomad EAS

AF:

0.436

Gnomad SAS

AF:

0.576

Gnomad FIN

AF:

0.467

Gnomad MID

AF:

0.583

Gnomad NFE

AF:

0.482

Gnomad OTH

AF:

0.510

GnomAD4 exome

AF:

0.485

AC:

156723

AN:

323062

Hom.:

38533

Cov.:

AF XY:

0.487

AC XY:

82009

AN XY:

168560

show subpopulations

Gnomad4 AFR exome

AF:

0.387

Gnomad4 AMR exome

AF:

0.564

Gnomad4 ASJ exome

AF:

0.556

Gnomad4 EAS exome

AF:

0.460

Gnomad4 SAS exome

AF:

0.583

Gnomad4 FIN exome

AF:

0.469

Gnomad4 NFE exome

AF:

0.480

Gnomad4 OTH exome

AF:

0.483

GnomAD4 genome

AF:

0.465

AC:

70564

AN:

151788

Hom.:

16619

Cov.:

AF XY:

0.469

AC XY:

34815

AN XY:

74154

show subpopulations

Gnomad4 AFR

AF:

0.388

Gnomad4 AMR

AF:

0.533

Gnomad4 ASJ

AF:

0.541

Gnomad4 EAS

AF:

0.436

Gnomad4 SAS

AF:

0.575

Gnomad4 FIN

AF:

0.467

Gnomad4 NFE

AF:

0.482

Gnomad4 OTH

AF:

0.514

Alfa

AF:

0.189

Hom.:

245

Bravo

AF:

0.469

ClinVar

Significance: Benign

Submissions summary: Benign:2Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Three Vessel Coronary Disease

Benign:1

Department of Cardiology, Chinese Academy of Medical Sciences, Fuwai Hospital

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

PECAM1 POLYMORPHISM

Benign:1

Feb 01, 1996

OMIM

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: literature only

- -

not provided

Other:1

ClinVar Staff, National Center for Biotechnology Information (NCBI)

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

CADD

Benign

6.7

LIST_S2

Benign

0.71

T;T;T;T

MetaRNN

Benign

0.0066

T;T;T;T

PROVEAN

Benign

0.0

N;N;N;N

Sift

Benign

0.21

T;T;T;T

Sift4G

Benign

0.12

T;.;.;.

Vest4

0.17

gMVP

0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over