dbSNP rs7297662: SUOX:c.-628G>A (chr12-56001594-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000394109(SUOX):c.-628G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 162,016 control chromosomes in the GnomAD database, including 17,609 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 0.46 ( 16296 hom., cov: 31)

Exomes 𝑓: 0.49 ( 1313 hom. )

Consequence

SUOX
ENST00000394109 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.197

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 links:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SUOX	NM_001032386.2 link	c.-10-618G>A	intron_variant	Intron 2 of 4	ENST00000266971.8	NP_001027558.1	P51687A0A024RB79
SUOX	NM_000456.3 link	c.-10-618G>A	intron_variant	Intron 3 of 5		NP_000447.2	P51687A0A024RB79
SUOX	NM_001032387.2 link	c.-10-618G>A	intron_variant	Intron 1 of 3		NP_001027559.1	P51687A0A024RB79

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUOX	ENST00000266971.8 link	c.-10-618G>A		intron_variant	Intron 2 of 4	2	NM_001032386.2	ENSP00000266971.3		P51687

Frequencies

GnomAD3 genomes

AF:

0.458

AC:

69528

AN:

151772

Hom.:

16275

Cov.:

show subpopulations

Gnomad AFR

AF:

0.384

Gnomad AMI

AF:

0.441

Gnomad AMR

AF:

0.612

Gnomad ASJ

AF:

0.481

Gnomad EAS

AF:

0.409

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.562

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.459

Gnomad OTH

AF:

0.492

GnomAD4 exome

AF:

0.488

AC:

4943

AN:

10126

Hom.:

1313

Cov.:

AF XY:

0.481

AC XY:

2452

AN XY:

5102

show subpopulations

Gnomad4 AFR exome

AF:

0.379

AC:

AN:

Gnomad4 AMR exome

AF:

0.657

AC:

1384

AN:

2106

Gnomad4 ASJ exome

AF:

0.466

AC:

AN:

Gnomad4 EAS exome

AF:

0.383

AC:

154

AN:

402

Gnomad4 SAS exome

AF:

0.373

AC:

410

AN:

1098

Gnomad4 FIN exome

AF:

0.506

AC:

AN:

172

Gnomad4 NFE exome

AF:

0.459

AC:

2654

AN:

5778

Gnomad4 Remaining exome

AF:

0.455

AC:

202

AN:

444

Heterozygous variant carriers

118

235

353

470

588

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

152

228

304

380

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.458

AC:

69574

AN:

151890

Hom.:

16296

Cov.:

AF XY:

0.465

AC XY:

34498

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.383

AC:

0.382982

AN:

0.382982

Gnomad4 AMR

AF:

0.613

AC:

0.612886

AN:

0.612886

Gnomad4 ASJ

AF:

0.481

AC:

0.481279

AN:

0.481279

Gnomad4 EAS

AF:

0.410

AC:

0.409674

AN:

0.409674

Gnomad4 SAS

AF:

0.385

AC:

0.384599

AN:

0.384599

Gnomad4 FIN

AF:

0.562

AC:

0.562453

AN:

0.562453

Gnomad4 NFE

AF:

0.459

AC:

0.45937

AN:

0.45937

Gnomad4 OTH

AF:

0.493

AC:

0.493359

AN:

0.493359

Heterozygous variant carriers

1888

3775

5663

7550

9438

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

628

1256

1884

2512

3140

<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:

0.471

Hom.:

28635

Bravo

AF:

0.468

Asia WGS

AF:

0.387

AC:

1348

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.8

DANN

Benign

0.76

Mutation Taster

=299/1

polymorphism (auto)

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