rs3917683

chr1-169622135-T-C

Variant summary

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

The NM_003005.4(SELP):c.4-2916A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 152,142 control chromosomes in the GnomAD database, including 25,066 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 0.57 (25066 hom., cov: 34)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SELP	NM_003005.4	c.4-2916A>G		intron_variant		ENST00000263686.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SELP	ENST00000263686.11	c.4-2916A>G		intron_variant		1	NM_003005.4	P1

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86370 AN: 152022 Hom.: 25029 Cov.: 34

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.568 AC: 86458 AN: 152142 Hom.: 25066 Cov.: 34 AF XY: 0.563 AC XY: 41882 AN XY: 74366

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.572

Alfa AF: 0.562 Hom.: 11105

Bravo AF: 0.568

Asia WGS AF: 0.417 AC: 1450 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.8
Dann	Benign	0.50

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: rs3917683; hg19: chr1-169591373;