chr1-169603407-C-T

Position:

• chr1-169603407-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.1520-196G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 150,822 control chromosomes in the GnomAD database, including 13,596 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 0.40 (13596 hom., cov: 30)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SELP	NM_003005.4	c.1520-196G>A		intron_variant		ENST00000263686.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SELP	ENST00000263686.11	c.1520-196G>A		intron_variant		1	NM_003005.4	P1

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60593 AN: 150704 Hom.: 13578 Cov.: 30

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.356

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.402 AC: 60646 AN: 150822 Hom.: 13596 Cov.: 30 AF XY: 0.418 AC XY: 30809 AN XY: 73626

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.415

Alfa AF: 0.380 Hom.: 23732

Bravo AF: 0.395

Asia WGS AF: 0.716 AC: 2485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2205895; hg19: chr1-169572645;