rs1805193

chr1-169733631-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000450.2(SELE):c.-19G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0913 in 1,610,688 control chromosomes in the GnomAD database, including 7,433 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 0.078 (563 hom., cov: 32)
  • Exomes 𝑓: 0.093 (6870 hom.)
• Consequence: SELE NM_000450.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SELE	NM_000450.2	c.-19G>T		5_prime_UTR_variant	2/14	ENST00000333360.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SELE	ENST00000333360.12	c.-19G>T		5_prime_UTR_variant	2/14	1	NM_000450.2	P1

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11855 AN: 152104 Hom.: 563 Cov.: 32

Gnomad AFR AF: 0.0389

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0644

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.0744

Gnomad FIN AF: 0.0721

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0855

GnomAD3 exomes AF: 0.0827 AC: 20742 AN: 250886 Hom.: 1068 AF XY: 0.0854 AC XY: 11580 AN XY: 135568

Gnomad AFR exome AF: 0.0368

Gnomad AMR exome AF: 0.0493

Gnomad ASJ exome AF: 0.147

Gnomad EAS exome AF: 0.0136

Gnomad SAS exome AF: 0.0840

Gnomad FIN exome AF: 0.0750

Gnomad NFE exome AF: 0.105

Gnomad OTH exome AF: 0.0977

GnomAD4 exome AF: 0.0927 AC: 135167 AN: 1458466 Hom.: 6870 Cov.: 31 AF XY: 0.0933 AC XY: 67735 AN XY: 725698

Gnomad4 AFR exome AF: 0.0359

Gnomad4 AMR exome AF: 0.0514

Gnomad4 ASJ exome AF: 0.141

Gnomad4 EAS exome AF: 0.0271

Gnomad4 SAS exome AF: 0.0808

Gnomad4 FIN exome AF: 0.0778

Gnomad4 NFE exome AF: 0.0987

Gnomad4 OTH exome AF: 0.0945

GnomAD4 genome AF: 0.0779 AC: 11857 AN: 152222 Hom.: 563 Cov.: 32 AF XY: 0.0757 AC XY: 5632 AN XY: 74412

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.0643

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0170

Gnomad4 SAS AF: 0.0744

Gnomad4 FIN AF: 0.0721

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.0957 Hom.: 373

Bravo AF: 0.0748

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	12
Dann	Benign	0.79

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

Publications

LitVar

Other links and lift over

dbSNP: rs1805193; hg19: chr1-169702772;