chr1-169607330-G-A

Position:

• chr1-169607330-G-A

Variant summary

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

The NM_003005.4(SELP):​c.1334-196C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,964 control chromosomes in the GnomAD database, including 12,160 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 0.36 (12160 hom., cov: 32)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.974

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SELP	NM_003005.4	c.1334-196C>T		intron_variant		ENST00000263686.11	NP_002996.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SELP	ENST00000263686.11	c.1334-196C>T		intron_variant		1	NM_003005.4	ENSP00000263686.5

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55433 AN: 151846 Hom.: 12156 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.365 AC: 55447 AN: 151964 Hom.: 12160 Cov.: 32 AF XY: 0.381 AC XY: 28325 AN XY: 74264

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.384

Alfa AF: 0.363 Hom.: 5857

Bravo AF: 0.356

Asia WGS AF: 0.703 AC: 2439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.14
DANN	Benign	0.60

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: rs3917751; hg19: chr1-169576568;