NM_003005.4:c.2438+407G>A

Variant names:

• chr1-169591019-C-T
• rs3917843
• NM_003005.4:c.2438+407G>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.2438+407G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0842 in 152,110 control chromosomes in the GnomAD database, including 1,718 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 0.084 (1718 hom., cov: 32)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 10 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELP	NM_003005.4	c.2438+407G>A		intron_variant	Intron 15 of 16	ENST00000263686.11	NP_002996.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELP	ENST00000263686.11	c.2438+407G>A		intron_variant	Intron 15 of 16	1	NM_003005.4	ENSP00000263686.5

Frequencies

GnomAD3 genomes AF: 0.0843 AC: 12811 AN: 151992 Hom.: 1720 Cov.: 32

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0606

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0537

Gnomad OTH AF: 0.0885

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

GnomAD4 genome AF: 0.0842 AC: 12809 AN: 152110 Hom.: 1718 Cov.: 32 AF XY: 0.0954 AC XY: 7094 AN XY: 74358

African (AFR) AF: 0.0132 AC: 550 AN: 41518

American (AMR) AF: 0.151 AC: 2300 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0606 AC: 210 AN: 3466

East Asian (EAS) AF: 0.657 AC: 3385 AN: 5156

South Asian (SAS) AF: 0.162 AC: 782 AN: 4816

European-Finnish (FIN) AF: 0.155 AC: 1641 AN: 10588

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.0537 AC: 3652 AN: 67976

Other (OTH) AF: 0.0938 AC: 198 AN: 2112

Alfa AF: 0.0771 Hom.: 221

Bravo AF: 0.0817

Asia WGS AF: 0.400 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.52
PhyloP100		-0.15
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: rs3917843; hg19: chr1-169560257;