1-169621556-A-G

Variant names:

• chr1-169621556-A-G
• rs3917691
• NM_003005.4:c.4-2337T>C

Variant summary

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

The NM_003005.4(SELP):​c.4-2337T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 151,684 control chromosomes in the GnomAD database, including 44,584 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 0.76 (44584 hom., cov: 29)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003005.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELP	NM_003005.4	MANE Select	c.4-2337T>C		intron	N/A	NP_002996.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELP	ENST00000263686.11	TSL:1 MANE Select	c.4-2337T>C		intron	N/A	ENSP00000263686.5
	SELP	ENST00000367786.6	TSL:5	c.4-2337T>C		intron	N/A	ENSP00000356760.1
	SELP	ENST00000367788.6	TSL:5	c.4-2337T>C		intron	N/A	ENSP00000356762.1

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115626 AN: 151566 Hom.: 44540 Cov.: 29

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.834

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.763 AC: 115715 AN: 151684 Hom.: 44584 Cov.: 29 AF XY: 0.755 AC XY: 55962 AN XY: 74084

African (AFR) AF: 0.865 AC: 35776 AN: 41340

American (AMR) AF: 0.674 AC: 10271 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2699 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3620 AN: 5138

South Asian (SAS) AF: 0.727 AC: 3499 AN: 4810

European-Finnish (FIN) AF: 0.659 AC: 6920 AN: 10496

Middle Eastern (MID) AF: 0.832 AC: 243 AN: 292

European-Non Finnish (NFE) AF: 0.742 AC: 50380 AN: 67874

Other (OTH) AF: 0.761 AC: 1605 AN: 2108

Alfa AF: 0.753 Hom.: 116258

Bravo AF: 0.768

Asia WGS AF: 0.714 AC: 2486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.056
DANN	Benign	0.36
PhyloP100		-2.3
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: rs3917691; hg19: chr1-169590794;