NM_000442.5:c.1916+128G>T

Variant names:

• chr17-64353363-C-A
• rs12944077
• NM_000442.5:c.1916+128G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000442.5(PECAM1):​c.1916+128G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 28)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PECAM1 NM_000442.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 4 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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (Cadd=2.195).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PECAM1	NM_000442.5	c.1916+128G>T		intron_variant	Intron 10 of 15	ENST00000563924.6	NP_000433.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PECAM1	ENST00000563924.6	c.1916+128G>T		intron_variant	Intron 10 of 15	1	NM_000442.5	ENSP00000457421.1

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 252782 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 127912

African (AFR) AF: 0.00 AC: 0 AN: 6852

American (AMR) AF: 0.00 AC: 0 AN: 7358

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9124

East Asian (EAS) AF: 0.00 AC: 0 AN: 22720

South Asian (SAS) AF: 0.00 AC: 0 AN: 2712

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30140

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1276

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 156450

Other (OTH) AF: 0.00 AC: 0 AN: 16150

GnomAD4 genome Cov.: 28

Alfa AF: 0.00 Hom.: 1206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	2.2
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs12944077; hg19: -;