17-64352183-G-A

Variant names:

• chr17-64352183-G-A
• rs4968624
• NM_000442.5:c.1990+207C>T

Variant summary

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

The NM_000442.5(PECAM1):​c.1990+207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,090 control chromosomes in the GnomAD database, including 14,374 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 (14374 hom., cov: 32)
• Consequence: PECAM1 NM_000442.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461
• 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=3.362).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PECAM1	NM_000442.5	MANE Select	c.1990+207C>T		intron	N/A	NP_000433.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PECAM1	ENST00000563924.6	TSL:1 MANE Select	c.1990+207C>T		intron	N/A	ENSP00000457421.1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62811 AN: 151972 Hom.: 14367 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.413 AC: 62845 AN: 152090 Hom.: 14374 Cov.: 32 AF XY: 0.419 AC XY: 31131 AN XY: 74320

African (AFR) AF: 0.200 AC: 8305 AN: 41500

American (AMR) AF: 0.516 AC: 7876 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1879 AN: 3472

East Asian (EAS) AF: 0.470 AC: 2433 AN: 5174

South Asian (SAS) AF: 0.579 AC: 2791 AN: 4824

European-Finnish (FIN) AF: 0.469 AC: 4945 AN: 10550

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32861 AN: 67998

Other (OTH) AF: 0.476 AC: 1005 AN: 2112

Alfa AF: 0.467 Hom.: 6492

Bravo AF: 0.410

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	3.4
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs4968624;