rs5359

Variant names:

• chr1-169723381-T-C
• rs5359
• NM_000450.2:c.*1144A>G

Variant summary

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

The NM_000450.2(SELE):​c.*1144A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,216 control chromosomes in the GnomAD database, including 2,973 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 (2973 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: SELE NM_000450.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.752
• Publications: 14 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELE	NM_000450.2	c.*1144A>G		3_prime_UTR_variant	Exon 14 of 14	ENST00000333360.12	NP_000441.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELE	ENST00000333360.12	c.*1144A>G		3_prime_UTR_variant	Exon 14 of 14	1	NM_000450.2	ENSP00000331736.7

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28580 AN: 152100 Hom.: 2962 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.210

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.188 AC: 28637 AN: 152216 Hom.: 2973 Cov.: 33 AF XY: 0.191 AC XY: 14184 AN XY: 74420

African (AFR) AF: 0.244 AC: 10124 AN: 41538

American (AMR) AF: 0.247 AC: 3771 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1302 AN: 5174

South Asian (SAS) AF: 0.236 AC: 1137 AN: 4828

European-Finnish (FIN) AF: 0.171 AC: 1815 AN: 10588

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.136 AC: 9219 AN: 68010

Other (OTH) AF: 0.213 AC: 450 AN: 2112

Alfa AF: 0.153 Hom.: 2160

Bravo AF: 0.199

Asia WGS AF: 0.250 AC: 867 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.48
PhyloP100		0.75
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: rs5359; hg19: chr1-169692522;