17-64323215-G-C

Position:

• chr17-64323215-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000442.5(PECAM1):​c.*601C>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 0.516 in 987,206 control chromosomes in the GnomAD database, including 132,253 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 (19325 hom., cov: 31)
  • Exomes 𝑓: 0.52 (112928 hom.)
• Consequence: PECAM1 NM_000442.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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/exons	MANE	UniProt
PECAM1	NM_000442.5	c.*601C>G		3_prime_UTR_variant	16/16	ENST00000563924.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PECAM1	ENST00000563924.6	c.*601C>G		3_prime_UTR_variant	16/16	1	NM_000442.5	P1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75384 AN: 151838 Hom.: 19316 Cov.: 31

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.523

GnomAD4 exome AF: 0.519 AC: 433474 AN: 835250 Hom.: 112928 Cov.: 31 AF XY: 0.520 AC XY: 200694 AN XY: 385828

Gnomad4 AFR exome AF: 0.349

Gnomad4 AMR exome AF: 0.594

Gnomad4 ASJ exome AF: 0.553

Gnomad4 EAS exome AF: 0.684

Gnomad4 SAS exome AF: 0.601

Gnomad4 FIN exome AF: 0.524

Gnomad4 NFE exome AF: 0.519

Gnomad4 OTH exome AF: 0.528

GnomAD4 genome AF: 0.496 AC: 75431 AN: 151956 Hom.: 19325 Cov.: 31 AF XY: 0.502 AC XY: 37253 AN XY: 74264

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.525

Alfa AF: 0.348 Hom.: 871

Bravo AF: 0.495

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6808; hg19: chr17-62400575;