dbSNP rs4072032: PECAM1:c.92-779C>T (chr17-64378896-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000442.5(PECAM1):c.92-779C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,112 control chromosomes in the GnomAD database, including 14,176 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 ( 14156 hom., cov: 31)

Exomes 𝑓: 0.52 ( 20 hom. )

Consequence

PECAM1
NM_000442.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0640

Variant links:

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]

PECAM1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (Cadd=3.898).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PECAM1	NM_000442.5 link	c.92-779C>T		intron_variant	Intron 2 of 15	ENST00000563924.6	NP_000433.4	P16284-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PECAM1	ENST00000563924.6 link	c.92-779C>T		intron_variant	Intron 2 of 15	1	NM_000442.5	ENSP00000457421.1		P16284-1

Frequencies

GnomAD3 genomes

AF:

0.411

AC:

62410

AN:

151866

Hom.:

14144

Cov.:

show subpopulations

Gnomad AFR

AF:

0.200

Gnomad AMI

AF:

0.643

Gnomad AMR

AF:

0.515

Gnomad ASJ

AF:

0.540

Gnomad EAS

AF:

0.437

Gnomad SAS

AF:

0.576

Gnomad FIN

AF:

0.467

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.482

Gnomad OTH

AF:

0.467

GnomAD4 exome

AF:

0.523

AC:

AN:

128

Hom.:

Cov.:

AF XY:

0.553

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.578

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.411

AC:

62452

AN:

151984

Hom.:

14156

Cov.:

AF XY:

0.417

AC XY:

30971

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.200

Gnomad4 AMR

AF:

0.515

Gnomad4 ASJ

AF:

0.540

Gnomad4 EAS

AF:

0.437

Gnomad4 SAS

AF:

0.576

Gnomad4 FIN

AF:

0.467

Gnomad4 NFE

AF:

0.482

Gnomad4 OTH

AF:

0.472

Alfa

AF:

0.423

Hom.:

1184

Bravo

AF:

0.407

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

CADD

Benign

3.9

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over