chr1-169603709-T-G

Variant names:

• chr1-169603709-T-G
• rs3917768
• NM_003005.4:c.1520-498A>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.1520-498A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,048 control chromosomes in the GnomAD database, including 15,932 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 0.43 (15932 hom., cov: 31)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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.1520-498A>C		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.1520-498A>C		intron	N/A	ENSP00000263686.5	P16109
	SELP	ENST00000426706.6	TSL:1	c.1517-498A>C		intron	N/A	ENSP00000391694.2	Q5R349
	SELP	ENST00000909597.1		c.1520-498A>C		intron	N/A	ENSP00000579656.1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65101 AN: 151930 Hom.: 15930 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.428 AC: 65111 AN: 152048 Hom.: 15932 Cov.: 31 AF XY: 0.442 AC XY: 32821 AN XY: 74292

African (AFR) AF: 0.232 AC: 9623 AN: 41480

American (AMR) AF: 0.557 AC: 8514 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1638 AN: 3470

East Asian (EAS) AF: 0.963 AC: 4971 AN: 5164

South Asian (SAS) AF: 0.569 AC: 2747 AN: 4824

European-Finnish (FIN) AF: 0.572 AC: 6028 AN: 10530

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30174 AN: 67992

Other (OTH) AF: 0.451 AC: 952 AN: 2112

Alfa AF: 0.356 Hom.: 2085

Bravo AF: 0.420

Asia WGS AF: 0.740 AC: 2573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.37
DANN	Benign	0.69
PhyloP100		-1.1
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: rs3917768; hg19: chr1-169572947;