rs3917836

Variant names:

• chr1-169592036-T-C
• rs3917836
• NM_003005.4:c.2408-580A>G

Variant summary

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

The NM_003005.4(SELP):​c.2408-580A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,204 control chromosomes in the GnomAD database, including 1,118 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 0.11 (1118 hom., cov: 32)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELP	NM_003005.4	c.2408-580A>G		intron_variant	Intron 14 of 16	ENST00000263686.11	NP_002996.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELP	ENST00000263686.11	c.2408-580A>G		intron_variant	Intron 14 of 16	1	NM_003005.4	ENSP00000263686.5

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16380 AN: 152086 Hom.: 1109 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00751

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0908

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.108 AC: 16416 AN: 152204 Hom.: 1118 Cov.: 32 AF XY: 0.105 AC XY: 7796 AN XY: 74418

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.0855

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.00752

Gnomad4 SAS AF: 0.0431

Gnomad4 FIN AF: 0.0382

Gnomad4 NFE AF: 0.0908

Gnomad4 OTH AF: 0.109

Alfa AF: 0.103 Hom.: 136

Bravo AF: 0.115

Asia WGS AF: 0.0520 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.4
DANN	Benign	0.43

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: rs3917836; hg19: chr1-169561274;