rs2070782

Variant names:

• chr17-64354771-C-T
• rs2070782
• NM_000442.5:c.1888+162G>A

Variant summary

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

The NM_000442.5(PECAM1):​c.1888+162G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,094 control chromosomes in the GnomAD database, including 13,023 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 0.38 (13023 hom., cov: 32)
• Consequence: PECAM1 NM_000442.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 3 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 (Cadd=2.394).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000442.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PECAM1	NM_000442.5	MANE Select	c.1888+162G>A		intron	N/A	NP_000433.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PECAM1	ENST00000563924.6	TSL:1 MANE Select	c.1888+162G>A		intron	N/A	ENSP00000457421.1	P16284-1
	PECAM1	ENST00000904885.1		c.1888+162G>A		intron	N/A	ENSP00000574944.1
	PECAM1	ENST00000904891.1		c.1888+162G>A		intron	N/A	ENSP00000574950.1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58214 AN: 151974 Hom.: 13030 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.366

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.383 AC: 58209 AN: 152094 Hom.: 13023 Cov.: 32 AF XY: 0.385 AC XY: 28583 AN XY: 74330

African (AFR) AF: 0.141 AC: 5849 AN: 41524

American (AMR) AF: 0.389 AC: 5936 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1477 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2718 AN: 5148

South Asian (SAS) AF: 0.415 AC: 2003 AN: 4824

European-Finnish (FIN) AF: 0.523 AC: 5528 AN: 10562

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33551 AN: 67976

Other (OTH) AF: 0.363 AC: 768 AN: 2114

Alfa AF: 0.462 Hom.: 6691

Bravo AF: 0.356

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	2.4
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs2070782;