1-169610140-C-T

Variant names:

• chr1-169610140-C-T
• rs3917739
• NM_003005.4:c.1148-451G>A

Variant summary

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

The NM_003005.4(SELP):​c.1148-451G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 151,440 control chromosomes in the GnomAD database, including 35,972 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 0.68 (35972 hom., cov: 29)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 11 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELP	NM_003005.4	c.1148-451G>A		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.1148-451G>A		intron_variant	Intron 7 of 16	1	NM_003005.4	ENSP00000263686.5

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103189 AN: 151324 Hom.: 35956 Cov.: 29

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.682 AC: 103245 AN: 151440 Hom.: 35972 Cov.: 29 AF XY: 0.678 AC XY: 50195 AN XY: 74000

African (AFR) AF: 0.830 AC: 34193 AN: 41210

American (AMR) AF: 0.606 AC: 9230 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2301 AN: 3464

East Asian (EAS) AF: 0.755 AC: 3884 AN: 5142

South Asian (SAS) AF: 0.641 AC: 3072 AN: 4796

European-Finnish (FIN) AF: 0.546 AC: 5702 AN: 10440

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42586 AN: 67860

Other (OTH) AF: 0.672 AC: 1405 AN: 2092

Alfa AF: 0.644 Hom.: 59823

Bravo AF: 0.691

Asia WGS AF: 0.672 AC: 2337 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.47
PhyloP100		1.4
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: rs3917739; hg19: chr1-169579378;