rs7297662
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
ENST00000394109.7 5_prime_UTR
Scores
2
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]
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ACMG classification
Classification made for transcript
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: 69528AN: 151772Hom.: 16275 Cov.: 31
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GnomAD4 exome AF: 0.488 AC: 4943AN: 10126Hom.: 1313 Cov.: 0 AF XY: 0.481 AC XY: 2452AN XY: 5102
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GnomAD4 genome ? AF: 0.458 AC: 69574AN: 151890Hom.: 16296 Cov.: 31 AF XY: 0.465 AC XY: 34498AN XY: 74238
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at