1-169611052-C-T

Position:

• chr1-169611052-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003005.4(SELP):​c.1147+440G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,878 control chromosomes in the GnomAD database, including 17,210 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 0.47 (17210 hom., cov: 31)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SELP	NM_003005.4	c.1147+440G>A		intron_variant		ENST00000263686.11	NP_002996.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SELP	ENST00000263686.11	c.1147+440G>A		intron_variant		1	NM_003005.4	ENSP00000263686.5

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71060 AN: 151758 Hom.: 17184 Cov.: 31

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.468 AC: 71114 AN: 151878 Hom.: 17210 Cov.: 31 AF XY: 0.459 AC XY: 34072 AN XY: 74202

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.487

Alfa AF: 0.453 Hom.: 16728

Bravo AF: 0.466

Asia WGS AF: 0.315 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.57
DANN	Benign	0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs2235302; hg19: chr1-169580290;