Variant 1-169727805-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_000450.2(SELE):c.1402C>T(p.His468Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 1,613,874 control chromosomes in the GnomAD database, including 11,098 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.11 ( 1089 hom., cov: 32)

Exomes 𝑓: 0.11 ( 10009 hom. )

Consequence

SELE
NM_000450.2 missense

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 0.480

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 (MetaRNN=0.0035199225).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SELE	NM_000450.2 link	c.1402C>T	p.His468Tyr	missense_variant	9/14	ENST00000333360.12	NP_000441.2	P16581

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SELE	ENST00000333360.12 link	c.1402C>T	p.His468Tyr	missense_variant	9/14	1	NM_000450.2	ENSP00000331736.7		P16581

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16504

AN:

152064

Hom.:

1084

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0752

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.0824

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.0958

Gnomad OTH

AF:

0.124

GnomAD3 exomes

AF:

0.145

AC:

36320

AN:

251050

Hom.:

3364

AF XY:

0.139

AC XY:

18921

AN XY:

135658

show subpopulations

Gnomad AFR exome

AF:

0.0732

Gnomad AMR exome

AF:

0.297

Gnomad ASJ exome

AF:

0.0843

Gnomad EAS exome

AF:

0.208

Gnomad SAS exome

AF:

0.147

Gnomad FIN exome

AF:

0.138

Gnomad NFE exome

AF:

0.105

Gnomad OTH exome

AF:

0.142

GnomAD4 exome

AF:

0.108

AC:

157241

AN:

1461692

Hom.:

10009

Cov.:

AF XY:

0.108

AC XY:

78778

AN XY:

727142

show subpopulations

Gnomad4 AFR exome

AF:

0.0727

Gnomad4 AMR exome

AF:

0.289

Gnomad4 ASJ exome

AF:

0.0857

Gnomad4 EAS exome

AF:

0.208

Gnomad4 SAS exome

AF:

0.146

Gnomad4 FIN exome

AF:

0.142

Gnomad4 NFE exome

AF:

0.0933

Gnomad4 OTH exome

AF:

0.111

GnomAD4 genome

AF:

0.109

AC:

16524

AN:

152182

Hom.:

1089

Cov.:

AF XY:

0.111

AC XY:

8253

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.0751

Gnomad4 AMR

AF:

0.195

Gnomad4 ASJ

AF:

0.0824

Gnomad4 EAS

AF:

0.209

Gnomad4 SAS

AF:

0.141

Gnomad4 FIN

AF:

0.137

Gnomad4 NFE

AF:

0.0958

Gnomad4 OTH

AF:

0.122

Alfa

AF:

0.106

Hom.:

2501

Bravo

AF:

0.115

TwinsUK

AF:

0.0965

AC:

358

ALSPAC

AF:

0.0960

AC:

370

ESP6500AA

AF:

0.0778

AC:

343

ESP6500EA

AF:

0.0949

AC:

816

ExAC

AF:

0.139

AC:

16905

Asia WGS

AF:

0.148

AC:

513

AN:

3476

EpiCase

AF:

0.103

EpiControl

AF:

0.102

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

IgA nephropathy, susceptibility to

Uncertain:1

Uncertain significance, no assertion criteria provided

literature only

OMIM

Jan 01, 2006

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.079

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.32

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.019

.;T;T

Eigen

Benign

0.079

Eigen_PC

Benign

0.0065

FATHMM_MKL

Benign

0.27

LIST_S2

Benign

0.064

T;T;T

MetaRNN

Benign

0.0035

T;T;T

MetaSVM

Benign

-0.83

MutationAssessor

Uncertain

2.3

.;.;M

PrimateAI

Benign

0.23

PROVEAN

Benign

-1.8

N;N;N

REVEL

Benign

0.18

Sift

Uncertain

0.018

D;D;T

Sift4G

Uncertain

0.039

D;T;T

Polyphen

0.94

.;.;P

Vest4

0.098

MPC

0.23

ClinPred

0.065

GERP RS

5.7

gMVP

0.18

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over