rs6504218

Variant names:

• chr17-64330939-A-G
• rs6504218
• NM_000442.5:c.2165-1217T>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.2165-1217T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,010 control chromosomes in the GnomAD database, including 23,142 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 (23142 hom., cov: 32)
• Consequence: PECAM1 NM_000442.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 24 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PECAM1	NM_000442.5	c.2165-1217T>C		intron_variant	Intron 14 of 15	ENST00000563924.6	NP_000433.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PECAM1	ENST00000563924.6	c.2165-1217T>C		intron_variant	Intron 14 of 15	1	NM_000442.5	ENSP00000457421.1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83666 AN: 151892 Hom.: 23129 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.551 AC: 83728 AN: 152010 Hom.: 23142 Cov.: 32 AF XY: 0.554 AC XY: 41143 AN XY: 74276

African (AFR) AF: 0.553 AC: 22936 AN: 41446

American (AMR) AF: 0.620 AC: 9468 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1922 AN: 3468

East Asian (EAS) AF: 0.688 AC: 3563 AN: 5176

South Asian (SAS) AF: 0.606 AC: 2920 AN: 4820

European-Finnish (FIN) AF: 0.537 AC: 5662 AN: 10548

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.521 AC: 35445 AN: 67974

Other (OTH) AF: 0.566 AC: 1193 AN: 2108

Alfa AF: 0.536 Hom.: 101109

Bravo AF: 0.559

Asia WGS AF: 0.638 AC: 2216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.8
DANN	Benign	0.75
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs6504218; hg19: chr17-62408299;