rs773126

chr12-56001636-T-Achr12-56001636-T-G

Variant summary

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

The ENST00000394109.7(SUOX):c.-586T>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 0.37 in 169,990 control chromosomes in the GnomAD database, including 13,036 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 0.37 (11556 hom., cov: 31)
  • Exomes 𝑓: 0.37 (1480 hom.)
• Consequence: SUOX ENST00000394109.7 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594

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=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUOX	NM_001032386.2	c.-10-576T>A		intron_variant		ENST00000266971.8
SUOX	NM_000456.3	c.-10-576T>A		intron_variant
SUOX	NM_001032387.2	c.-10-576T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUOX	ENST00000266971.8	c.-10-576T>A		intron_variant		2	NM_001032386.2	P1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56302 AN: 151842 Hom.: 11554 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.390

GnomAD4 exome AF: 0.368 AC: 6639 AN: 18030 Hom.: 1480 Cov.: 1 AF XY: 0.361 AC XY: 3293 AN XY: 9122

Gnomad4 AFR exome AF: 0.236

Gnomad4 AMR exome AF: 0.293

Gnomad4 ASJ exome AF: 0.403

Gnomad4 EAS exome AF: 0.00703

Gnomad4 SAS exome AF: 0.278

Gnomad4 FIN exome AF: 0.384

Gnomad4 NFE exome AF: 0.442

Gnomad4 OTH exome AF: 0.433

GnomAD4 genome AF: 0.371 AC: 56317 AN: 151960 Hom.: 11556 Cov.: 31 AF XY: 0.366 AC XY: 27213 AN XY: 74290

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.386

Alfa AF: 0.287 Hom.: 802

Bravo AF: 0.356

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	7.8
Dann	Benign	0.74

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: rs773126; hg19: chr12-56395420;