rs368327991
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001032386.2(SUOX):c.50+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00009 in 1,610,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000088 ( 0 hom. )
Consequence
SUOX
NM_001032386.2 intron
NM_001032386.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.256
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 12-56002280-G-A is Benign according to our data. Variant chr12-56002280-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 309831.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SUOX | NM_001032386.2 | c.50+9G>A | intron_variant | ENST00000266971.8 | NP_001027558.1 | |||
| SUOX | NM_000456.3 | c.50+9G>A | intron_variant | NP_000447.2 | ||||
| SUOX | NM_001032387.2 | c.50+9G>A | intron_variant | NP_001027559.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SUOX | ENST00000266971.8 | c.50+9G>A | intron_variant | 2 | NM_001032386.2 | ENSP00000266971 | P1 |
Frequencies
GnomAD3 genomes 0.000105 AC: 16AN: 152198Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000193 AC: 48AN: 248260Hom.: 0 AF XY: 0.000193 AC XY: 26AN XY: 134418
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GnomAD4 exome AF: 0.0000885 AC: 129AN: 1458222Hom.: 0 Cov.: 31 AF XY: 0.0000827 AC XY: 60AN XY: 725616
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GnomAD4 genome 0.000105 AC: 16AN: 152316Hom.: 0 Cov.: 31 AF XY: 0.000134 AC XY: 10AN XY: 74478
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Sulfite oxidase deficiency Uncertain:1Benign:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
| Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 27, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at