1-169600680-A-T

Position:

• chr1-169600680-A-T

Variant summary

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

The NM_003005.4(SELP):​c.1705+2346T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,112 control chromosomes in the GnomAD database, including 11,659 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 0.34 (11659 hom., cov: 32)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SELP	NM_003005.4	c.1705+2346T>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.1705+2346T>A		intron_variant		1	NM_003005.4	ENSP00000263686.5

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52436 AN: 151994 Hom.: 11654 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.345 AC: 52450 AN: 152112 Hom.: 11659 Cov.: 32 AF XY: 0.362 AC XY: 26886 AN XY: 74342

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.369

Alfa AF: 0.352 Hom.: 1471

Bravo AF: 0.333

Asia WGS AF: 0.697 AC: 2419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.80

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: rs2420378; hg19: chr1-169569918;