1-169598278-T-A

Position:

• chr1-169598278-T-A

Variant summary

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

The NM_003005.4(SELP):​c.1706-1102A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,164 control chromosomes in the GnomAD database, including 5,275 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 0.25 (5275 hom., cov: 33)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SELP	NM_003005.4	c.1706-1102A>T		intron_variant		ENST00000263686.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SELP	ENST00000263686.11	c.1706-1102A>T		intron_variant		1	NM_003005.4	P1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37391 AN: 152046 Hom.: 5262 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.246 AC: 37408 AN: 152164 Hom.: 5275 Cov.: 33 AF XY: 0.251 AC XY: 18686 AN XY: 74388

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.257

Alfa AF: 0.264 Hom.: 780

Bravo AF: 0.239

Asia WGS AF: 0.275 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.92
DANN	Benign	0.67

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: rs2298903; hg19: chr1-169567516;