chr1-169630016-T-C

Position:

• chr1-169630016-T-C

Variant summary

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

The NM_003005.4(SELP):​c.3+56A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 1,610,560 control chromosomes in the GnomAD database, including 206,585 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 0.52 (21453 hom., cov: 32)
  • Exomes 𝑓: 0.50 (185132 hom.)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

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 (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SELP	NM_003005.4	c.3+56A>G		intron_variant		ENST00000263686.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SELP	ENST00000263686.11	c.3+56A>G		intron_variant		1	NM_003005.4	P1

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79478 AN: 151908 Hom.: 21420 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.526

GnomAD4 exome AF: 0.500 AC: 729521 AN: 1458534 Hom.: 185132 AF XY: 0.497 AC XY: 360603 AN XY: 725678

Gnomad4 AFR exome AF: 0.641

Gnomad4 AMR exome AF: 0.388

Gnomad4 ASJ exome AF: 0.556

Gnomad4 EAS exome AF: 0.321

Gnomad4 SAS exome AF: 0.394

Gnomad4 FIN exome AF: 0.465

Gnomad4 NFE exome AF: 0.515

Gnomad4 OTH exome AF: 0.508

GnomAD4 genome AF: 0.523 AC: 79559 AN: 152026 Hom.: 21453 Cov.: 32 AF XY: 0.517 AC XY: 38416 AN XY: 74300

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.525

Alfa AF: 0.509 Hom.: 26047

Bravo AF: 0.528

Asia WGS AF: 0.356 AC: 1239 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	4.9
DANN	Benign	0.41

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: rs732314; hg19: chr1-169599254;