chr1-169605819-G-T

Variant names:

• chr1-169605819-G-T
• rs3766126
• NM_003005.4:c.1519+1130C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003005.4(SELP):​c.1519+1130C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,042 control chromosomes in the GnomAD database, including 10,678 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 0.33 (10678 hom., cov: 32)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELP	NM_003005.4	c.1519+1130C>A		intron_variant	Intron 9 of 16	ENST00000263686.11	NP_002996.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELP	ENST00000263686.11	c.1519+1130C>A		intron_variant	Intron 9 of 16	1	NM_003005.4	ENSP00000263686.5

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49763 AN: 151922 Hom.: 10670 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.327 AC: 49781 AN: 152042 Hom.: 10678 Cov.: 32 AF XY: 0.344 AC XY: 25595 AN XY: 74324

African (AFR) AF: 0.117 AC: 4867 AN: 41494

American (AMR) AF: 0.475 AC: 7245 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3472

East Asian (EAS) AF: 0.953 AC: 4942 AN: 5186

South Asian (SAS) AF: 0.515 AC: 2485 AN: 4824

European-Finnish (FIN) AF: 0.513 AC: 5407 AN: 10538

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22596 AN: 67956

Other (OTH) AF: 0.351 AC: 741 AN: 2112

Alfa AF: 0.319 Hom.: 1143

Bravo AF: 0.318

Asia WGS AF: 0.691 AC: 2398 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.65
PhyloP100		0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3766126; hg19: chr1-169575057;