NM_000442.5:c.1916+128G>A

Variant names:

• chr17-64353363-C-T
• rs12944077
• NM_000442.5:c.1916+128G>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.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
• Publications: 4 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=2.618).
• 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 rank	MANE	Protein	UniProt
PECAM1	NM_000442.5	c.1916+128G>A		intron_variant	Intron 10 of 15	ENST00000563924.6	NP_000433.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PECAM1	ENST00000563924.6	c.1916+128G>A		intron_variant	Intron 10 of 15	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

African (AFR) AF: 0.148 AC: 1013 AN: 6848

American (AMR) AF: 0.400 AC: 2938 AN: 7346

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 3788 AN: 9118

East Asian (EAS) AF: 0.481 AC: 10914 AN: 22702

South Asian (SAS) AF: 0.398 AC: 1079 AN: 2708

European-Finnish (FIN) AF: 0.526 AC: 15831 AN: 30082

Middle Eastern (MID) AF: 0.319 AC: 407 AN: 1276

European-Non Finnish (NFE) AF: 0.491 AC: 76761 AN: 156246

Other (OTH) AF: 0.439 AC: 7079 AN: 16126

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

African (AFR) AF: 0.145 AC: 5799 AN: 40022

American (AMR) AF: 0.390 AC: 5873 AN: 15070

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1475 AN: 3466

East Asian (EAS) AF: 0.531 AC: 2717 AN: 5118

South Asian (SAS) AF: 0.415 AC: 1982 AN: 4774

European-Finnish (FIN) AF: 0.525 AC: 5448 AN: 10370

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

European-Non Finnish (NFE) AF: 0.493 AC: 33374 AN: 67760

Other (OTH) AF: 0.367 AC: 764 AN: 2080

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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs12944077; hg19: -;