rs17522707

Variant names:

• chr1-169593824-G-A
• rs17522707
• NM_003005.4:c.2288-100C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-169593824-G-A
• chr1-169593824-G-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.2288-100C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0878 in 1,163,380 control chromosomes in the GnomAD database, including 4,845 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 0.067 (447 hom., cov: 32)
  • Exomes 𝑓: 0.091 (4398 hom.)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.099 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELP	NM_003005.4	c.2288-100C>T		intron_variant	Intron 13 of 16	ENST00000263686.11	NP_002996.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELP	ENST00000263686.11	c.2288-100C>T		intron_variant	Intron 13 of 16	1	NM_003005.4	ENSP00000263686.5

Frequencies

GnomAD3 genomes AF: 0.0670 AC: 10190 AN: 152068 Hom.: 446 Cov.: 32

Gnomad AFR AF: 0.0184

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00731

Gnomad SAS AF: 0.0403

Gnomad FIN AF: 0.0595

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0779

GnomAD4 exome AF: 0.0910 AC: 91972 AN: 1011194 Hom.: 4398 AF XY: 0.0906 AC XY: 46184 AN XY: 509644

African (AFR) AF: 0.0175 AC: 410 AN: 23468

American (AMR) AF: 0.0549 AC: 1702 AN: 31000

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 2168 AN: 19076

East Asian (EAS) AF: 0.0121 AC: 426 AN: 35298

South Asian (SAS) AF: 0.0447 AC: 2615 AN: 58498

European-Finnish (FIN) AF: 0.0709 AC: 2799 AN: 39492

Middle Eastern (MID) AF: 0.0937 AC: 435 AN: 4644

European-Non Finnish (NFE) AF: 0.103 AC: 77768 AN: 755582

Other (OTH) AF: 0.0827 AC: 3649 AN: 44136

GnomAD4 genome AF: 0.0669 AC: 10186 AN: 152186 Hom.: 447 Cov.: 32 AF XY: 0.0642 AC XY: 4778 AN XY: 74392

African (AFR) AF: 0.0184 AC: 765 AN: 41534

American (AMR) AF: 0.0633 AC: 967 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 418 AN: 3472

East Asian (EAS) AF: 0.00733 AC: 38 AN: 5184

South Asian (SAS) AF: 0.0405 AC: 195 AN: 4812

European-Finnish (FIN) AF: 0.0595 AC: 630 AN: 10594

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6867 AN: 68002

Other (OTH) AF: 0.0762 AC: 161 AN: 2114

Alfa AF: 0.0822 Hom.: 108

Bravo AF: 0.0644

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.32
PhyloP100		-0.99
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: rs17522707; hg19: chr1-169563062; COSMIC: COSV55260458; COSMIC: COSV55260458;