Variant rs1044032 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_021199.4(SQOR):c.791T>C(p.Ile264Thr) variant causes a missense change. The variant allele was found at a frequency of 0.217 in 1,613,820 control chromosomes in the GnomAD database, including 41,217 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.20 ( 3295 hom., cov: 32)

Exomes 𝑓: 0.22 ( 37922 hom. )

Consequence

SQOR
NM_021199.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.23

Variant links:

Genes affected

SQOR (HGNC:20390): (sulfide quinone oxidoreductase) The protein encoded by this gene may function in mitochondria to catalyze the conversion of sulfide to persulfides, thereby decreasing toxic concencrations of sulfide. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Sep 2012]

SQOR links:

ENSG00000260170 (HGNC:):

ENSG00000260170 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=0.001188308).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SQOR	NM_021199.4 linkuse as main transcript	c.791T>C	p.Ile264Thr	missense_variant	6/10	ENST00000260324.12	NP_067022.1	Q9Y6N5A0A024R5X2
SQOR	NM_001271213.2 linkuse as main transcript	c.791T>C	p.Ile264Thr	missense_variant	7/11		NP_001258142.1	Q9Y6N5A0A024R5X2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SQOR	ENST00000260324.12 linkuse as main transcript	c.791T>C	p.Ile264Thr	missense_variant	6/10	1	NM_021199.4	ENSP00000260324.7	Q9Y6N5
ENSG00000260170	ENST00000564080.1 linkuse as main transcript	c.791T>C	p.Ile264Thr	missense_variant	6/6	3		ENSP00000455047.1	H3BNX3
SQOR	ENST00000568606.5 linkuse as main transcript	c.791T>C	p.Ile264Thr	missense_variant	7/11	5		ENSP00000456019.1	Q9Y6N5

Frequencies

GnomAD3 genomes

AF:

0.197

AC:

29957

AN:

151932

Hom.:

3288

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.262

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.206

Gnomad EAS

AF:

0.426

Gnomad SAS

AF:

0.363

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.204

Gnomad OTH

AF:

0.202

GnomAD3 exomes

AF:

0.245

AC:

61459

AN:

251202

Hom.:

8473

AF XY:

0.250

AC XY:

33947

AN XY:

135780

show subpopulations

Gnomad AFR exome

AF:

0.113

Gnomad AMR exome

AF:

0.231

Gnomad ASJ exome

AF:

0.220

Gnomad EAS exome

AF:

0.443

Gnomad SAS exome

AF:

0.371

Gnomad FIN exome

AF:

0.256

Gnomad NFE exome

AF:

0.202

Gnomad OTH exome

AF:

0.235

GnomAD4 exome

AF:

0.219

AC:

320272

AN:

1461770

Hom.:

37922

Cov.:

AF XY:

0.223

AC XY:

162432

AN XY:

727184

show subpopulations

Gnomad4 AFR exome

AF:

0.110

Gnomad4 AMR exome

AF:

0.228

Gnomad4 ASJ exome

AF:

0.218

Gnomad4 EAS exome

AF:

0.433

Gnomad4 SAS exome

AF:

0.364

Gnomad4 FIN exome

AF:

0.255

Gnomad4 NFE exome

AF:

0.201

Gnomad4 OTH exome

AF:

0.233

GnomAD4 genome

AF:

0.197

AC:

29970

AN:

152050

Hom.:

3295

Cov.:

AF XY:

0.202

AC XY:

15036

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.112

Gnomad4 AMR

AF:

0.220

Gnomad4 ASJ

AF:

0.206

Gnomad4 EAS

AF:

0.426

Gnomad4 SAS

AF:

0.363

Gnomad4 FIN

AF:

0.254

Gnomad4 NFE

AF:

0.204

Gnomad4 OTH

AF:

0.208

Alfa

AF:

0.210

Hom.:

8977

Bravo

AF:

0.192

TwinsUK

AF:

0.196

AC:

726

ALSPAC

AF:

0.196

AC:

756

ESP6500AA

AF:

0.111

AC:

490

ESP6500EA

AF:

0.204

AC:

1756

ExAC

AF:

0.243

AC:

29486

Asia WGS

AF:

0.389

AC:

1353

AN:

3478

EpiCase

AF:

0.212

EpiControl

AF:

0.205

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.083

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.40

.;T;T

Eigen

Benign

-0.24

Eigen_PC

Benign

-0.061

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Benign

0.68

T;.;T

MetaRNN

Benign

0.0012

T;T;T

MetaSVM

Benign

-0.95

PrimateAI

Benign

0.34

PROVEAN

Uncertain

-3.2

D;D;D

REVEL

Benign

0.14

Sift

Benign

0.095

T;T;T

Sift4G

Benign

0.13

T;T;T

Polyphen

0.0060

.;B;B

Vest4

0.071, 0.075

MPC

0.084

ClinPred

0.049

GERP RS

4.6

Varity_R

0.38

gMVP

0.61

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