rs2235304

Variant names:

• chr1-169610515-G-A
• rs2235304
• NM_003005.4:c.1148-826C>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.1148-826C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 152,106 control chromosomes in the GnomAD database, including 399 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 0.060 (399 hom., cov: 32)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 1 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 = 0.184 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.1148-826C>T		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.1148-826C>T		intron	N/A	ENSP00000263686.5
	SELP	ENST00000426706.6	TSL:1	c.1145-826C>T		intron	N/A	ENSP00000391694.2
	SELP	ENST00000367786.6	TSL:5	c.962-826C>T		intron	N/A	ENSP00000356760.1

Frequencies

GnomAD3 genomes AF: 0.0597 AC: 9069 AN: 151988 Hom.: 400 Cov.: 32

Gnomad AFR AF: 0.0238

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0498

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0916

Gnomad FIN AF: 0.0825

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0644

Gnomad OTH AF: 0.0736

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

GnomAD4 genome AF: 0.0596 AC: 9063 AN: 152106 Hom.: 399 Cov.: 32 AF XY: 0.0608 AC XY: 4520 AN XY: 74358

African (AFR) AF: 0.0237 AC: 982 AN: 41456

American (AMR) AF: 0.0497 AC: 760 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3472

East Asian (EAS) AF: 0.194 AC: 1007 AN: 5180

South Asian (SAS) AF: 0.0925 AC: 446 AN: 4822

European-Finnish (FIN) AF: 0.0825 AC: 872 AN: 10576

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0644 AC: 4378 AN: 68002

Other (OTH) AF: 0.0714 AC: 151 AN: 2114

Alfa AF: 0.0665 Hom.: 638

Bravo AF: 0.0561

Asia WGS AF: 0.144 AC: 500 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	0.77
DANN	Benign	0.30
PhyloP100		-1.8
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: rs2235304; hg19: chr1-169579753;