rs2236866

chr1-169627075-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003005.4(SELP):c.3+2997T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,910 control chromosomes in the GnomAD database, including 26,072 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 0.58 (26072 hom., cov: 31)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

Genes affected

SELP (HGNC:10721): (selectin P) This gene encodes a 140 kDa protein that is stored in the alpha-granules of platelets and Weibel-Palade bodies of endothelial cells. This protein redistributes to the plasma membrane during platelet activation and degranulation and mediates the interaction of activated endothelial cells or platelets with leukocytes. The membrane protein is a calcium-dependent receptor that binds to sialylated forms of Lewis blood group carbohydrate antigens on neutrophils and monocytes. Alternative splice variants may occur but are not well documented. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SELP	NM_003005.4	c.3+2997T>A		intron_variant		ENST00000263686.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SELP	ENST00000263686.11	c.3+2997T>A		intron_variant		1	NM_003005.4	P1

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87857 AN: 151792 Hom.: 26035 Cov.: 31

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.582

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.579 AC: 87943 AN: 151910 Hom.: 26072 Cov.: 31 AF XY: 0.573 AC XY: 42564 AN XY: 74236

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.581

Alfa AF: 0.557 Hom.: 13348

Bravo AF: 0.579

Asia WGS AF: 0.424 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.4
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2236866; hg19: chr1-169596313;