NM_000442.5:c.*601C>G

Variant names:

• chr17-64323215-G-C
• rs6808
• NM_000442.5:c.*601C>G

Variant summary

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

The NM_000442.5(PECAM1):​c.*601C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 987,206 control chromosomes in the GnomAD database, including 132,253 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 0.50 (19325 hom., cov: 31)
  • Exomes 𝑓: 0.52 (112928 hom.)
• Consequence: PECAM1 NM_000442.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 12 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 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.*601C>G		3_prime_UTR	Exon 16 of 16	NP_000433.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PECAM1	ENST00000563924.6	TSL:1 MANE Select	c.*601C>G		3_prime_UTR	Exon 16 of 16	ENSP00000457421.1	P16284-1
	PECAM1	ENST00000904885.1		c.*601C>G		3_prime_UTR	Exon 17 of 17	ENSP00000574944.1
	PECAM1	ENST00000904891.1		c.*601C>G		3_prime_UTR	Exon 17 of 17	ENSP00000574950.1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75384 AN: 151838 Hom.: 19316 Cov.: 31

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.523

GnomAD4 exome AF: 0.519 AC: 433474 AN: 835250 Hom.: 112928 Cov.: 31 AF XY: 0.520 AC XY: 200694 AN XY: 385828

African (AFR) AF: 0.349 AC: 5513 AN: 15792

American (AMR) AF: 0.594 AC: 854 AN: 1438

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 2852 AN: 5156

East Asian (EAS) AF: 0.684 AC: 2505 AN: 3660

South Asian (SAS) AF: 0.601 AC: 10007 AN: 16654

European-Finnish (FIN) AF: 0.524 AC: 151 AN: 288

Middle Eastern (MID) AF: 0.616 AC: 998 AN: 1620

European-Non Finnish (NFE) AF: 0.519 AC: 396125 AN: 763242

Other (OTH) AF: 0.528 AC: 14469 AN: 27400

GnomAD4 genome AF: 0.496 AC: 75431 AN: 151956 Hom.: 19325 Cov.: 31 AF XY: 0.502 AC XY: 37253 AN XY: 74264

African (AFR) AF: 0.363 AC: 15049 AN: 41426

American (AMR) AF: 0.597 AC: 9102 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1888 AN: 3464

East Asian (EAS) AF: 0.689 AC: 3544 AN: 5146

South Asian (SAS) AF: 0.605 AC: 2918 AN: 4820

European-Finnish (FIN) AF: 0.538 AC: 5683 AN: 10560

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35529 AN: 67974

Other (OTH) AF: 0.525 AC: 1107 AN: 2108

Alfa AF: 0.348 Hom.: 871

Bravo AF: 0.495

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.37
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs6808; hg19: chr17-62400575;