rs3917682

Variant names:

• chr1-169622310-A-C
• rs3917682
• NM_003005.4:c.4-3091T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-169622310-A-C
• chr1-169622310-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003005.4(SELP):​c.4-3091T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,164 control chromosomes in the GnomAD database, including 7,768 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 0.29 (7768 hom., cov: 33)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELP	NM_003005.4	c.4-3091T>G		intron_variant	Intron 1 of 16	ENST00000263686.11	NP_002996.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELP	ENST00000263686.11	c.4-3091T>G		intron_variant	Intron 1 of 16	1	NM_003005.4	ENSP00000263686.5

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44570 AN: 152046 Hom.: 7768 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.293 AC: 44570 AN: 152164 Hom.: 7768 Cov.: 33 AF XY: 0.287 AC XY: 21375 AN XY: 74382

African (AFR) AF: 0.115 AC: 4778 AN: 41546

American (AMR) AF: 0.257 AC: 3925 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1531 AN: 3472

East Asian (EAS) AF: 0.207 AC: 1074 AN: 5182

South Asian (SAS) AF: 0.258 AC: 1246 AN: 4832

European-Finnish (FIN) AF: 0.327 AC: 3459 AN: 10576

Middle Eastern (MID) AF: 0.465 AC: 134 AN: 288

European-Non Finnish (NFE) AF: 0.403 AC: 27389 AN: 67964

Other (OTH) AF: 0.332 AC: 701 AN: 2114

Alfa AF: 0.217 Hom.: 700

Bravo AF: 0.282

Asia WGS AF: 0.216 AC: 749 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3917682; hg19: chr1-169591548;