Genetic Variant SUOX:c.-10-1042A>G (chr12-56001170-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001032386.2(SUOX):c.-10-1042A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 125,774 control chromosomes in the GnomAD database, including 10,446 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 0.42 ( 10445 hom., cov: 18)

Exomes 𝑓: 0.21 ( 1 hom. )

Consequence

SUOX
NM_001032386.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.624

Publications

46 publications found

Variant links:

Genes affected

SUOX (HGNC:11460): (sulfite oxidase) Sulfite oxidase is a homodimeric protein localized to the intermembrane space of mitochondria. Each subunit contains a heme domain and a molybdopterin-binding domain. The enzyme catalyzes the oxidation of sulfite to sulfate, the final reaction in the oxidative degradation of the sulfur amino acids cysteine and methionine. Sulfite oxidase deficiency results in neurological abnormalities which are often fatal at an early age. Alternative splicing results in multiple transcript variants encoding identical proteins. [provided by RefSeq, Jul 2008]

SUOX Gene-Disease associations (from GenCC):

isolated sulfite oxidase deficiency
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia, Ambry Genetics, ClinGen

SUOX links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001032386.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SUOX	NM_001032386.2	MANE Select	c.-10-1042A>G	intron	N/A	NP_001027558.1	P51687
SUOX	NM_000456.3		c.-10-1042A>G	intron	N/A	NP_000447.2	P51687
SUOX	NM_001032387.2		c.-10-1042A>G	intron	N/A	NP_001027559.1	P51687

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SUOX	ENST00000266971.8	TSL:2 MANE Select	c.-10-1042A>G	intron	N/A	ENSP00000266971.3	P51687
SUOX	ENST00000356124.8	TSL:1	c.-10-1042A>G	intron	N/A	ENSP00000348440.4	P51687
SUOX	ENST00000552813.5	TSL:1	n.132-1042A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.417

AC:

52363

AN:

125656

Hom.:

10426

Cov.:

show subpopulations

Gnomad AFR

AF:

0.474

Gnomad AMI

AF:

0.582

Gnomad AMR

AF:

0.375

Gnomad ASJ

AF:

0.402

Gnomad EAS

AF:

0.265

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.420

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.409

Gnomad OTH

AF:

0.395

GnomAD4 exome

AF:

0.206

AC:

AN:

Hom.:

AF XY:

0.208

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.208

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.595

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.417

AC:

52428

AN:

125740

Hom.:

10445

Cov.:

AF XY:

0.415

AC XY:

24617

AN XY:

59350

show subpopulations

African (AFR)

AF:

0.474

AC:

15805

AN:

33332

American (AMR)

AF:

0.375

AC:

3992

AN:

10646

Ashkenazi Jewish (ASJ)

AF:

0.402

AC:

1314

AN:

3268

East Asian (EAS)

AF:

0.264

AC:

1007

AN:

3814

South Asian (SAS)

AF:

0.289

AC:

1091

AN:

3776

European-Finnish (FIN)

AF:

0.420

AC:

2557

AN:

6084

Middle Eastern (MID)

AF:

0.438

AC:

AN:

192

European-Non Finnish (NFE)

AF:

0.409

AC:

25413

AN:

62080

Other (OTH)

AF:

0.396

AC:

676

AN:

1708

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

1471

2942

4412

5883

7354

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

510

1020

1530

2040

2550

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.382

Hom.:

1192

Bravo

AF:

0.393

Asia WGS

AF:

0.248

AC:

864

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

1.9

(source)

DANN

Benign

0.68

PhyloP100

-0.62

PromoterAI

-0.019

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over