1-169595507-G-A

Variant names:

• chr1-169595507-G-A
• rs3917820
• NM_003005.4:c.2101+418C>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.2101+418C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,158 control chromosomes in the GnomAD database, including 7,078 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 0.23 (7078 hom., cov: 33)
• Consequence: SELP NM_003005.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• 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 = 0.546 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELP	NM_003005.4	MANE Select	c.2101+418C>T		intron	N/A	NP_002996.2	P16109

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SELP	ENST00000263686.11	TSL:1 MANE Select	c.2101+418C>T		intron	N/A	ENSP00000263686.5	P16109
	SELP	ENST00000426706.6	TSL:1	c.2098+418C>T		intron	N/A	ENSP00000391694.2	Q5R349
	SELP	ENST00000909597.1		c.2101+418C>T		intron	N/A	ENSP00000579656.1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34613 AN: 152040 Hom.: 7064 Cov.: 33

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0856

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0772

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.228 AC: 34673 AN: 152158 Hom.: 7078 Cov.: 33 AF XY: 0.220 AC XY: 16335 AN XY: 74386

African (AFR) AF: 0.552 AC: 22904 AN: 41476

American (AMR) AF: 0.143 AC: 2184 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0856 AC: 297 AN: 3468

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5186

South Asian (SAS) AF: 0.0257 AC: 124 AN: 4828

European-Finnish (FIN) AF: 0.0772 AC: 818 AN: 10602

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7874 AN: 67996

Other (OTH) AF: 0.202 AC: 427 AN: 2112

Alfa AF: 0.139 Hom.: 622

Bravo AF: 0.251

Asia WGS AF: 0.0530 AC: 187 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	2.5
DANN	Benign	0.44
PhyloP100		0.14
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: rs3917820; hg19: chr1-169564745;