1-169603407-C-T

Variant names:

• chr1-169603407-C-T
• rs2205895
• NM_003005.4:c.1520-196G>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.1520-196G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 150,822 control chromosomes in the GnomAD database, including 13,596 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 0.40 (13596 hom., cov: 30)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 28 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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.1520-196G>A		intron	N/A	NP_002996.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELP	ENST00000263686.11	TSL:1 MANE Select	c.1520-196G>A		intron	N/A	ENSP00000263686.5
	SELP	ENST00000426706.6	TSL:1	c.1517-196G>A		intron	N/A	ENSP00000391694.2
	SELP	ENST00000909597.1		c.1520-196G>A		intron	N/A	ENSP00000579656.1

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60593 AN: 150704 Hom.: 13578 Cov.: 30

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.356

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.402 AC: 60646 AN: 150822 Hom.: 13596 Cov.: 30 AF XY: 0.418 AC XY: 30809 AN XY: 73626

African (AFR) AF: 0.304 AC: 12404 AN: 40798

American (AMR) AF: 0.515 AC: 7825 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1433 AN: 3464

East Asian (EAS) AF: 0.959 AC: 4970 AN: 5182

South Asian (SAS) AF: 0.533 AC: 2546 AN: 4780

European-Finnish (FIN) AF: 0.545 AC: 5638 AN: 10352

Middle Eastern (MID) AF: 0.358 AC: 103 AN: 288

European-Non Finnish (NFE) AF: 0.363 AC: 24630 AN: 67782

Other (OTH) AF: 0.415 AC: 867 AN: 2090

Alfa AF: 0.378 Hom.: 36094

Bravo AF: 0.395

Asia WGS AF: 0.716 AC: 2485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.64
PhyloP100		0.38
Mutation Taster		=19/81	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2205895; hg19: chr1-169572645;