ENST00000909597.1:c.*1071A>C

Variant names:

• chr1-169588496-T-G
• rs1018828
• ENST00000909597.1:c.*1071A>C

Variant summary

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

The ENST00000909597.1(SELP):​c.*1071A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,252 control chromosomes in the GnomAD database, including 1,098 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 0.11 (1098 hom., cov: 32)
• Consequence: SELP ENST00000909597.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000909597.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELP	ENST00000909597.1		c.*1071A>C		3_prime_UTR	Exon 17 of 17	ENSP00000579656.1
	SELP	ENST00000909598.1		c.*967A>C		3_prime_UTR	Exon 16 of 16	ENSP00000579657.1
	SELP	ENST00000909599.1		c.*1071A>C		3_prime_UTR	Exon 16 of 16	ENSP00000579658.1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16087 AN: 152134 Hom.: 1089 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00769

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.0379

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.106 AC: 16123 AN: 152252 Hom.: 1098 Cov.: 32 AF XY: 0.103 AC XY: 7659 AN XY: 74448

African (AFR) AF: 0.181 AC: 7495 AN: 41494

American (AMR) AF: 0.0808 AC: 1236 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3470

East Asian (EAS) AF: 0.00770 AC: 40 AN: 5192

South Asian (SAS) AF: 0.0431 AC: 208 AN: 4828

European-Finnish (FIN) AF: 0.0379 AC: 402 AN: 10618

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0878 AC: 5973 AN: 68022

Other (OTH) AF: 0.106 AC: 225 AN: 2116

Alfa AF: 0.0944 Hom.: 2940

Bravo AF: 0.113

Asia WGS AF: 0.0520 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.42
PhyloP100		0.015

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1018828; hg19: chr1-169557734;