rs1805193

Variant names:

• chr1-169733631-C-A
• rs1805193
• NM_000450.2:c.-19G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 53 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=-0.72).
• 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 rank	MANE	Protein	UniProt
SELE	NM_000450.2	c.-19G>T		5_prime_UTR_variant	Exon 2 of 14	ENST00000333360.12	NP_000441.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELE	ENST00000333360.12	c.-19G>T		5_prime_UTR_variant	Exon 2 of 14	1	NM_000450.2	ENSP00000331736.7

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

GnomAD2 exomes AF: 0.0827 AC: 20742 AN: 250886 AF XY: 0.0854

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 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

African (AFR) AF: 0.0359 AC: 1201 AN: 33454

American (AMR) AF: 0.0514 AC: 2300 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 3680 AN: 26102

East Asian (EAS) AF: 0.0271 AC: 1076 AN: 39680

South Asian (SAS) AF: 0.0808 AC: 6961 AN: 86180

European-Finnish (FIN) AF: 0.0778 AC: 4151 AN: 53380

Middle Eastern (MID) AF: 0.115 AC: 661 AN: 5764

European-Non Finnish (NFE) AF: 0.0987 AC: 109440 AN: 1108928

Other (OTH) AF: 0.0945 AC: 5697 AN: 60264

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

African (AFR) AF: 0.0390 AC: 1619 AN: 41542

American (AMR) AF: 0.0643 AC: 984 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3470

East Asian (EAS) AF: 0.0170 AC: 88 AN: 5180

South Asian (SAS) AF: 0.0744 AC: 359 AN: 4824

European-Finnish (FIN) AF: 0.0721 AC: 764 AN: 10600

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7219 AN: 68002

Other (OTH) AF: 0.0837 AC: 176 AN: 2104

Alfa AF: 0.0951 Hom.: 422

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
PhyloP100		0.083
PromoterAI		-0.0054	Neutral
Mutation Taster		=300/0	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: rs1805193; hg19: chr1-169702772;