rs2244529

Variant names:

• chr1-169617794-A-G
• rs2244529
• NM_003005.4:c.95-380T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-169617794-A-G
• chr1-169617794-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003005.4(SELP):​c.95-380T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,082 control chromosomes in the GnomAD database, including 12,437 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 0.38 (12437 hom., cov: 32)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 14 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 (AFR) allele frequency at 95% confidence interval = 0.581 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.95-380T>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.95-380T>C		intron	N/A	ENSP00000263686.5
	SELP	ENST00000426706.6	TSL:1	c.92-380T>C		intron	N/A	ENSP00000391694.2
	SELP	ENST00000909597.1		c.95-380T>C		intron	N/A	ENSP00000579656.1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57761 AN: 151964 Hom.: 12400 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.380 AC: 57851 AN: 152082 Hom.: 12437 Cov.: 32 AF XY: 0.381 AC XY: 28328 AN XY: 74338

African (AFR) AF: 0.587 AC: 24364 AN: 41480

American (AMR) AF: 0.308 AC: 4705 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1143 AN: 3468

East Asian (EAS) AF: 0.349 AC: 1807 AN: 5176

South Asian (SAS) AF: 0.371 AC: 1786 AN: 4820

European-Finnish (FIN) AF: 0.328 AC: 3461 AN: 10562

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.286 AC: 19459 AN: 67978

Other (OTH) AF: 0.363 AC: 767 AN: 2114

Alfa AF: 0.315 Hom.: 14257

Bravo AF: 0.388

Asia WGS AF: 0.369 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.95
DANN	Benign	0.81
PhyloP100		-0.30
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: rs2244529; hg19: chr1-169587032;