rs2236868

Variant names:

• chr1-169614758-G-A
• rs2236868
• NM_003005.4:c.482-1065C>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.482-1065C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,030 control chromosomes in the GnomAD database, including 11,358 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 0.38 (11358 hom., cov: 32)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51
• Publications: 12 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELP	NM_003005.4	c.482-1065C>T		intron_variant	Intron 3 of 16	ENST00000263686.11	NP_002996.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELP	ENST00000263686.11	c.482-1065C>T		intron_variant	Intron 3 of 16	1	NM_003005.4	ENSP00000263686.5

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57178 AN: 151912 Hom.: 11358 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.376 AC: 57186 AN: 152030 Hom.: 11358 Cov.: 32 AF XY: 0.368 AC XY: 27373 AN XY: 74316

African (AFR) AF: 0.268 AC: 11132 AN: 41474

American (AMR) AF: 0.308 AC: 4694 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1655 AN: 3472

East Asian (EAS) AF: 0.213 AC: 1102 AN: 5184

South Asian (SAS) AF: 0.368 AC: 1776 AN: 4820

European-Finnish (FIN) AF: 0.396 AC: 4185 AN: 10562

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31221 AN: 67942

Other (OTH) AF: 0.409 AC: 865 AN: 2116

Alfa AF: 0.431 Hom.: 23456

Bravo AF: 0.365

Asia WGS AF: 0.277 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.074
DANN	Benign	0.23
PhyloP100		-2.5
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: rs2236868; hg19: chr1-169583996;