17-64353363-C-T

Position:

• chr17-64353363-C-T

Variant summary

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

The NM_000442.5(PECAM1):​c.1916+128G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 402,316 control chromosomes in the GnomAD database, including 42,206 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 0.39 (12912 hom., cov: 28)
  • Exomes 𝑓: 0.47 (29294 hom.)
• Consequence: PECAM1 NM_000442.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

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 (Cadd=2.618).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PECAM1	NM_000442.5	c.1916+128G>A		intron_variant		ENST00000563924.6	NP_000433.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PECAM1	ENST00000563924.6	c.1916+128G>A		intron_variant		1	NM_000442.5	ENSP00000457421.1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 57820 AN: 149748 Hom.: 12919 Cov.: 28

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.370

GnomAD4 exome AF: 0.475 AC: 119810 AN: 252452 Hom.: 29294 AF XY: 0.477 AC XY: 60898 AN XY: 127748

Gnomad4 AFR exome AF: 0.148

Gnomad4 AMR exome AF: 0.400

Gnomad4 ASJ exome AF: 0.415

Gnomad4 EAS exome AF: 0.481

Gnomad4 SAS exome AF: 0.398

Gnomad4 FIN exome AF: 0.526

Gnomad4 NFE exome AF: 0.491

Gnomad4 OTH exome AF: 0.439

GnomAD4 genome AF: 0.386 AC: 57814 AN: 149864 Hom.: 12912 Cov.: 28 AF XY: 0.387 AC XY: 28344 AN XY: 73172

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.367

Alfa AF: 0.392 Hom.: 1206

Bravo AF: 0.356

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	2.6

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12944077; hg19: -;