chr1-169621926-T-C

Variant names:

• chr1-169621926-T-C
• rs3917686
• NM_003005.4:c.4-2707A>G

Variant summary

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

The NM_003005.4(SELP):​c.4-2707A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,122 control chromosomes in the GnomAD database, including 5,102 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 0.21 (5102 hom., cov: 33)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELP	NM_003005.4	MANE Select	c.4-2707A>G		intron	N/A	NP_002996.2	P16109

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELP	ENST00000263686.11	TSL:1 MANE Select	c.4-2707A>G		intron	N/A	ENSP00000263686.5	P16109
	SELP	ENST00000909597.1		c.4-2707A>G		intron	N/A	ENSP00000579656.1
	SELP	ENST00000909601.1		c.4-2707A>G		intron	N/A	ENSP00000579660.1

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32016 AN: 152004 Hom.: 5077 Cov.: 33

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.211 AC: 32095 AN: 152122 Hom.: 5102 Cov.: 33 AF XY: 0.212 AC XY: 15765 AN XY: 74350

African (AFR) AF: 0.450 AC: 18657 AN: 41464

American (AMR) AF: 0.182 AC: 2780 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3470

East Asian (EAS) AF: 0.137 AC: 710 AN: 5178

South Asian (SAS) AF: 0.129 AC: 622 AN: 4822

European-Finnish (FIN) AF: 0.132 AC: 1394 AN: 10576

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7069 AN: 68010

Other (OTH) AF: 0.175 AC: 369 AN: 2108

Alfa AF: 0.138 Hom.: 2718

Bravo AF: 0.225

Asia WGS AF: 0.146 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.72
PhyloP100		0.38
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: rs3917686; hg19: chr1-169591164;