rs10489181

Variant names:

• chr1-169743456-T-C
• rs10489181
• ENST00000609271.1:c.-201-9333A>G

Variant summary

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

The ENST00000609271.1(SELE):​c.-201-9333A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,116 control chromosomes in the GnomAD database, including 3,978 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 0.20 (3978 hom., cov: 31)
• Consequence: SELE ENST00000609271.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 4 publications found

Genes affected

SELE (HGNC:10718): (selectin E) The protein encoded by this gene is found in cytokine-stimulated endothelial cells and is thought to be responsible for the accumulation of blood leukocytes at sites of inflammation by mediating the adhesion of cells to the vascular lining. It exhibits structural features such as the presence of lectin- and EGF-like domains followed by short consensus repeat (SCR) domains that contain 6 conserved cysteine residues. These proteins are part of the selectin family of cell adhesion molecules. Adhesion molecules participate in the interaction between leukocytes and the endothelium and appear to be involved in the pathogenesis of atherosclerosis. [provided by RefSeq, Jul 2008]

FIRRM (HGNC:25565): (FIGNL1 interacting regulator of recombination and mitosis)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELE	ENST00000609271.1	c.-201-9333A>G		intron_variant	Intron 1 of 2	4		ENSP00000476784.1
FIRRM	ENST00000498289.5	n.852-40355T>C		intron_variant	Intron 3 of 28	2

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30306 AN: 151998 Hom.: 3963 Cov.: 31

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0987

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.200 AC: 30379 AN: 152116 Hom.: 3978 Cov.: 31 AF XY: 0.205 AC XY: 15241 AN XY: 74382

African (AFR) AF: 0.324 AC: 13451 AN: 41476

American (AMR) AF: 0.266 AC: 4059 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3464

East Asian (EAS) AF: 0.434 AC: 2248 AN: 5176

South Asian (SAS) AF: 0.181 AC: 873 AN: 4826

European-Finnish (FIN) AF: 0.196 AC: 2079 AN: 10594

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0987 AC: 6708 AN: 67984

Other (OTH) AF: 0.205 AC: 434 AN: 2112

Alfa AF: 0.144 Hom.: 443

Bravo AF: 0.216

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.036
DANN	Benign	0.43
PhyloP100		-1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10489181; hg19: chr1-169712597;