rs4072032

chr17-64378896-G-A

Variant summary

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

The NM_000442.5(PECAM1):c.92-779C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,112 control chromosomes in the GnomAD database, including 14,176 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 0.41 (14156 hom., cov: 31)
  • Exomes 𝑓: 0.52 (20 hom.)
• Consequence: PECAM1 NM_000442.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

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=3.898).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PECAM1	NM_000442.5	c.92-779C>T		intron_variant		ENST00000563924.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PECAM1	ENST00000563924.6	c.92-779C>T		intron_variant		1	NM_000442.5	P1

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62410 AN: 151866 Hom.: 14144 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.467

GnomAD4 exome AF: 0.523 AC: 67 AN: 128 Hom.: 20 Cov.: 0 AF XY: 0.553 AC XY: 52 AN XY: 94

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.578

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.411 AC: 62452 AN: 151984 Hom.: 14156 Cov.: 31 AF XY: 0.417 AC XY: 30971 AN XY: 74282

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.472

Alfa AF: 0.423 Hom.: 1184

Bravo AF: 0.407

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Cadd	Benign	3.9

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4072032; hg19: -;