chr1-169611272-C-T

Variant names:

• chr1-169611272-C-T
• rs3917733
• NM_003005.4:c.1147+220G>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.1147+220G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,088 control chromosomes in the GnomAD database, including 3,559 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 0.19 (3559 hom., cov: 32)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 3 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.276 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.1147+220G>A		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.1147+220G>A		intron	N/A	ENSP00000263686.5
	SELP	ENST00000426706.6	TSL:1	c.1144+220G>A		intron	N/A	ENSP00000391694.2
	SELP	ENST00000367786.6	TSL:5	c.961+945G>A		intron	N/A	ENSP00000356760.1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29533 AN: 151970 Hom.: 3559 Cov.: 32

Gnomad AFR AF: 0.0809

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.194 AC: 29525 AN: 152088 Hom.: 3559 Cov.: 32 AF XY: 0.188 AC XY: 14015 AN XY: 74376

African (AFR) AF: 0.0808 AC: 3349 AN: 41466

American (AMR) AF: 0.174 AC: 2663 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3470

East Asian (EAS) AF: 0.00405 AC: 21 AN: 5184

South Asian (SAS) AF: 0.136 AC: 654 AN: 4826

European-Finnish (FIN) AF: 0.203 AC: 2144 AN: 10584

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19013 AN: 67960

Other (OTH) AF: 0.214 AC: 453 AN: 2114

Alfa AF: 0.235 Hom.: 1004

Bravo AF: 0.187

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.5
DANN	Benign	0.78
PhyloP100		0.27
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: rs3917733; hg19: chr1-169580510;