NM_003005.4:c.95-294A>G

Variant names:

• chr1-169617708-T-C
• rs2244526
• NM_003005.4:c.95-294A>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.95-294A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,170 control chromosomes in the GnomAD database, including 1,358 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 0.13 (1358 hom., cov: 32)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.173 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.95-294A>G		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.95-294A>G		intron	N/A	ENSP00000263686.5
	SELP	ENST00000426706.6	TSL:1	c.92-294A>G		intron	N/A	ENSP00000391694.2
	SELP	ENST00000909597.1		c.95-294A>G		intron	N/A	ENSP00000579656.1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19344 AN: 152052 Hom.: 1352 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.127 AC: 19375 AN: 152170 Hom.: 1358 Cov.: 32 AF XY: 0.130 AC XY: 9697 AN XY: 74406

African (AFR) AF: 0.176 AC: 7307 AN: 41488

American (AMR) AF: 0.151 AC: 2305 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0744 AC: 258 AN: 3470

East Asian (EAS) AF: 0.137 AC: 707 AN: 5176

South Asian (SAS) AF: 0.123 AC: 595 AN: 4822

European-Finnish (FIN) AF: 0.127 AC: 1351 AN: 10598

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0955 AC: 6492 AN: 68002

Other (OTH) AF: 0.110 AC: 232 AN: 2114

Alfa AF: 0.104 Hom.: 1118

Bravo AF: 0.132

Asia WGS AF: 0.124 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.69
PhyloP100		-0.043
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: rs2244526; hg19: chr1-169586946;