rs3917740

Variant names:

• chr1-169610028-G-A
• rs3917740
• NM_003005.4:c.1148-339C>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.1148-339C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,882 control chromosomes in the GnomAD database, including 5,533 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 0.25 (5533 hom., cov: 32)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.978
• Publications: 14 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 (AFR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELP	NM_003005.4	c.1148-339C>T		intron_variant	Intron 7 of 16	ENST00000263686.11	NP_002996.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELP	ENST00000263686.11	c.1148-339C>T		intron_variant	Intron 7 of 16	1	NM_003005.4	ENSP00000263686.5

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37786 AN: 151764 Hom.: 5510 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.249 AC: 37855 AN: 151882 Hom.: 5533 Cov.: 32 AF XY: 0.244 AC XY: 18116 AN XY: 74272

African (AFR) AF: 0.411 AC: 16990 AN: 41320

American (AMR) AF: 0.146 AC: 2225 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3466

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5174

South Asian (SAS) AF: 0.205 AC: 988 AN: 4812

European-Finnish (FIN) AF: 0.174 AC: 1839 AN: 10566

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13452 AN: 67954

Other (OTH) AF: 0.215 AC: 454 AN: 2112

Alfa AF: 0.211 Hom.: 6933

Bravo AF: 0.254

Asia WGS AF: 0.194 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.087
DANN	Benign	0.55
PhyloP100		-0.98
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: rs3917740; hg19: chr1-169579266;