rs5359

Positions:

• chr1-169723381-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• 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/exons	MANE	Protein	UniProt
SELE	NM_000450.2	c.*1144A>G		3_prime_UTR_variant	14/14	ENST00000333360.12	NP_000441.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SELE	ENST00000333360.12	c.*1144A>G		3_prime_UTR_variant	14/14	1	NM_000450.2	ENSP00000331736	P1

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

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

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.213

Alfa AF: 0.152 Hom.: 1786

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

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: rs5359; hg19: chr1-169692522;