rs7297662

Positions:

• chr12-56001594-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000394109.7(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 ENST00000394109.7 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

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]

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	UniProt
SUOX	NM_001032386.2	c.-10-618G>A		intron_variant		ENST00000266971.8
SUOX	NM_000456.3	c.-10-618G>A		intron_variant
SUOX	NM_001032387.2	c.-10-618G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUOX	ENST00000266971.8	c.-10-618G>A		intron_variant		2	NM_001032386.2	P1

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69528 AN: 151772 Hom.: 16275 Cov.: 31

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.: 0 AF XY: 0.481 AC XY: 2452 AN XY: 5102

Gnomad4 AFR exome AF: 0.379

Gnomad4 AMR exome AF: 0.657

Gnomad4 ASJ exome AF: 0.466

Gnomad4 EAS exome AF: 0.383

Gnomad4 SAS exome AF: 0.373

Gnomad4 FIN exome AF: 0.506

Gnomad4 NFE exome AF: 0.459

Gnomad4 OTH exome AF: 0.455

GnomAD4 genome AF: 0.458 AC: 69574 AN: 151890 Hom.: 16296 Cov.: 31 AF XY: 0.465 AC XY: 34498 AN XY: 74238

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.493

Alfa AF: 0.470 Hom.: 22469

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

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

Other links and lift over

dbSNP: rs7297662; hg19: chr12-56395378;