chr1-169599460-T-G

Variant names:

• chr1-169599460-T-G
• rs760694
• NM_003005.4:c.1706-2284A>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.1706-2284A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,006 control chromosomes in the GnomAD database, including 25,071 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 0.56 (25071 hom., cov: 32)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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.1706-2284A>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.1706-2284A>C		intron	N/A	ENSP00000263686.5
	SELP	ENST00000426706.6	TSL:1	c.1703-2284A>C		intron	N/A	ENSP00000391694.2
	SELP	ENST00000367786.6	TSL:5	c.1520-2284A>C		intron	N/A	ENSP00000356760.1

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85138 AN: 151890 Hom.: 25045 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.561 AC: 85212 AN: 152006 Hom.: 25071 Cov.: 32 AF XY: 0.569 AC XY: 42263 AN XY: 74276

African (AFR) AF: 0.674 AC: 27920 AN: 41400

American (AMR) AF: 0.623 AC: 9511 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1481 AN: 3468

East Asian (EAS) AF: 0.956 AC: 4956 AN: 5186

South Asian (SAS) AF: 0.545 AC: 2628 AN: 4818

European-Finnish (FIN) AF: 0.586 AC: 6191 AN: 10562

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.456 AC: 30997 AN: 67982

Other (OTH) AF: 0.555 AC: 1173 AN: 2112

Alfa AF: 0.494 Hom.: 49145

Bravo AF: 0.574

Asia WGS AF: 0.746 AC: 2591 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.70
PhyloP100		-0.79
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: rs760694; hg19: chr1-169568698;