rs2070783

Variant names:

• chr17-64329611-A-G
• rs2070783
• NM_000442.5:c.2187+89T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 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 (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 rank	MANE	Protein	UniProt
PECAM1	NM_000442.5	c.2187+89T>C		intron_variant	Intron 15 of 15	ENST00000563924.6	NP_000433.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PECAM1	ENST00000563924.6	c.2187+89T>C		intron_variant	Intron 15 of 15	1	NM_000442.5	ENSP00000457421.1

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

African (AFR) AF: 0.551 AC: 8625 AN: 15664

American (AMR) AF: 0.630 AC: 21764 AN: 34556

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 11281 AN: 19816

East Asian (EAS) AF: 0.753 AC: 24088 AN: 31970

South Asian (SAS) AF: 0.602 AC: 37494 AN: 62298

European-Finnish (FIN) AF: 0.532 AC: 25994 AN: 48900

Middle Eastern (MID) AF: 0.684 AC: 2767 AN: 4046

European-Non Finnish (NFE) AF: 0.531 AC: 165283 AN: 311340

Other (OTH) AF: 0.554 AC: 16869 AN: 30446

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

African (AFR) AF: 0.546 AC: 22657 AN: 41482

American (AMR) AF: 0.620 AC: 9477 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1926 AN: 3464

East Asian (EAS) AF: 0.737 AC: 3811 AN: 5172

South Asian (SAS) AF: 0.608 AC: 2933 AN: 4826

European-Finnish (FIN) AF: 0.542 AC: 5722 AN: 10566

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35956 AN: 67994

Other (OTH) AF: 0.571 AC: 1203 AN: 2108

Alfa AF: 0.535 Hom.: 5624

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
PhyloP100		0.053

Splicing

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

Other links and lift over

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