chr17-64323215-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000442.5(PECAM1):​c.*601C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000294 in 987,526 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000046 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000026 (0 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

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>A		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>A		3_prime_UTR	Exon 16 of 16	ENSP00000457421.1	P16284-1
	PECAM1	ENST00000904885.1		c.*601C>A		3_prime_UTR	Exon 17 of 17	ENSP00000574944.1
	PECAM1	ENST00000904891.1		c.*601C>A		3_prime_UTR	Exon 17 of 17	ENSP00000574950.1

Frequencies

GnomAD3 genomes AF: 0.0000461 AC: 7 AN: 151906 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000328

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000263 AC: 22 AN: 835502 Hom.: 0 Cov.: 31 AF XY: 0.0000363 AC XY: 14 AN XY: 385930

African (AFR) AF: 0.00 AC: 0 AN: 15798

American (AMR) AF: 0.00 AC: 0 AN: 1440

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5158

East Asian (EAS) AF: 0.000546 AC: 2 AN: 3662

South Asian (SAS) AF: 0.000180 AC: 3 AN: 16660

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 288

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1620

European-Non Finnish (NFE) AF: 0.0000223 AC: 17 AN: 763470

Other (OTH) AF: 0.00 AC: 0 AN: 27406

GnomAD4 genome AF: 0.0000460 AC: 7 AN: 152024 Hom.: 0 Cov.: 31 AF XY: 0.0000808 AC XY: 6 AN XY: 74300

African (AFR) AF: 0.00 AC: 0 AN: 41450

American (AMR) AF: 0.000328 AC: 5 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5146

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10572

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 67988

Other (OTH) AF: 0.00 AC: 0 AN: 2108

Alfa AF: 0.00 Hom.: 871

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.16
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;