chr17-64323758-T-C

Variant names:

• chr17-64323758-T-C
• rs2812
• NM_000442.5:c.*58A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000442.5(PECAM1):​c.*58A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 1,196,738 control chromosomes in the GnomAD database, including 171,266 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.50 (19329 hom., cov: 32)
  • Exomes 𝑓: 0.53 (151937 hom.)
• Consequence: PECAM1 NM_000442.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 30 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PECAM1	NM_000442.5	c.*58A>G		3_prime_UTR_variant	Exon 16 of 16	ENST00000563924.6	NP_000433.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PECAM1	ENST00000563924.6	c.*58A>G		3_prime_UTR_variant	Exon 16 of 16	1	NM_000442.5	ENSP00000457421.1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75390 AN: 151882 Hom.: 19319 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.523

GnomAD4 exome AF: 0.535 AC: 558417 AN: 1044736 Hom.: 151937 Cov.: 14 AF XY: 0.538 AC XY: 289773 AN XY: 538452

African (AFR) AF: 0.356 AC: 9091 AN: 25508

American (AMR) AF: 0.622 AC: 27078 AN: 43528

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 13047 AN: 23380

East Asian (EAS) AF: 0.694 AC: 26167 AN: 37718

South Asian (SAS) AF: 0.601 AC: 46599 AN: 77560

European-Finnish (FIN) AF: 0.528 AC: 28019 AN: 53046

Middle Eastern (MID) AF: 0.659 AC: 3285 AN: 4986

European-Non Finnish (NFE) AF: 0.519 AC: 380430 AN: 732434

Other (OTH) AF: 0.530 AC: 24701 AN: 46576

GnomAD4 genome AF: 0.496 AC: 75439 AN: 152002 Hom.: 19329 Cov.: 32 AF XY: 0.502 AC XY: 37264 AN XY: 74288

African (AFR) AF: 0.363 AC: 15032 AN: 41462

American (AMR) AF: 0.597 AC: 9114 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1889 AN: 3470

East Asian (EAS) AF: 0.689 AC: 3561 AN: 5166

South Asian (SAS) AF: 0.606 AC: 2921 AN: 4820

European-Finnish (FIN) AF: 0.539 AC: 5689 AN: 10564

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35518 AN: 67942

Other (OTH) AF: 0.525 AC: 1104 AN: 2104

Alfa AF: 0.523 Hom.: 71050

Bravo AF: 0.495

Asia WGS AF: 0.632 AC: 2197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6
DANN	Benign	0.65
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2812; hg19: chr17-62401118; COSMIC: COSV50535345;