rs12944077

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-64353363-C-A
• chr17-64353363-C-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).

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.1916+128G>T		intron	N/A	NP_000433.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PECAM1	ENST00000563924.6	TSL:1 MANE Select	c.1916+128G>T		intron	N/A	ENSP00000457421.1	P16284-1
	PECAM1	ENST00000904885.1		c.1916+128G>T		intron	N/A	ENSP00000574944.1
	PECAM1	ENST00000904891.1		c.1916+128G>T		intron	N/A	ENSP00000574950.1

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12944077;