rs2070783

Positions:

• chr17-64329611-A-G

Variant summary

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

The NM_000442.5(PECAM1):​c.2187+89T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 711,130 control chromosomes in the GnomAD database, including 113,246 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 0.55 (23485 hom., cov: 32)
  • Exomes 𝑓: 0.56 (89761 hom.)
• Consequence: PECAM1 NM_000442.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PECAM1	NM_000442.5	c.2187+89T>C		intron_variant		ENST00000563924.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PECAM1	ENST00000563924.6	c.2187+89T>C		intron_variant		1	NM_000442.5	P1

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84247 AN: 151976 Hom.: 23475 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.570

GnomAD4 exome AF: 0.562 AC: 314165 AN: 559036 Hom.: 89761 AF XY: 0.564 AC XY: 169638 AN XY: 300590

Gnomad4 AFR exome AF: 0.551

Gnomad4 AMR exome AF: 0.630

Gnomad4 ASJ exome AF: 0.569

Gnomad4 EAS exome AF: 0.753

Gnomad4 SAS exome AF: 0.602

Gnomad4 FIN exome AF: 0.532

Gnomad4 NFE exome AF: 0.531

Gnomad4 OTH exome AF: 0.554

GnomAD4 genome AF: 0.554 AC: 84306 AN: 152094 Hom.: 23485 Cov.: 32 AF XY: 0.558 AC XY: 41467 AN XY: 74328

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.571

Alfa AF: 0.535 Hom.: 3124

Bravo AF: 0.562

Asia WGS AF: 0.656 AC: 2279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2070783; hg19: chr17-62406971; COSMIC: COSV67895502;