dbSNP rs1805193: SELE:c.-19G>T (chr1-169733631-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0830

Variant links:

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]

SELE links:

C1orf112 (HGNC:25565): (FIGNL1 interacting regulator of recombination and mitosis)

C1orf112 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 rank	MANE	Protein	UniProt
SELE	NM_000450.2 link	c.-19G>T		5_prime_UTR_variant	Exon 2 of 14	ENST00000333360.12	NP_000441.2	P16581

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELE	ENST00000333360.12 link	c.-19G>T		5_prime_UTR_variant	Exon 2 of 14	1	NM_000450.2	ENSP00000331736.7		P16581

Frequencies

GnomAD3 genomes

AF:

0.0779

AC:

11855

AN:

152104

Hom.:

563

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.0933

AC XY:

67735

AN XY:

725698

show subpopulations

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.:

AF XY:

0.0757

AC XY:

5632

AN XY:

74412

show subpopulations

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

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over