rs4786

Positions:

• chr1-169722991-T-C
• chr1-169722991-T-G

Variant summary

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

The NM_000450.2(SELE):​c.*1534A>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 0.364 in 152,046 control chromosomes in the GnomAD database, including 11,093 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 0.36 (11093 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SELE NM_000450.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SELE	NM_000450.2	c.*1534A>G		3_prime_UTR_variant	14/14	ENST00000333360.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SELE	ENST00000333360.12	c.*1534A>G		3_prime_UTR_variant	14/14	1	NM_000450.2	P1

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55285 AN: 151928 Hom.: 11057 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.374

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.364 AC: 55376 AN: 152046 Hom.: 11093 Cov.: 32 AF XY: 0.370 AC XY: 27469 AN XY: 74334

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.375

Alfa AF: 0.285 Hom.: 11660

Bravo AF: 0.377

Asia WGS AF: 0.482 AC: 1679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.46

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: rs4786; hg19: chr1-169692132;