rs5750373
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021126.8(MPST):c.656-226G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 544,600 control chromosomes in the GnomAD database, including 56,266 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 0.49 ( 21030 hom., cov: 32)
Exomes 𝑓: 0.41 ( 35236 hom. )
Consequence
MPST
NM_021126.8 intron
NM_021126.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.06
Genes affected
MPST (HGNC:7223): (mercaptopyruvate sulfurtransferase) This protein encoded by this gene catalyzes the transfer of a sulfur ion from 3-mercaptopyruvate to cyanide or other thiol compounds. It may be involved in cysteine degradation and cyanide detoxification. There is confusion in literature between this protein (mercaptopyruvate sulfurtransferase, MPST), which appears to be cytoplasmic, and thiosulfate sulfurtransferase (rhodanese, TST, GeneID:7263), which is a mitochondrial protein. Deficiency in MPST activity has been implicated in a rare inheritable disorder known as mercaptolactate-cysteine disulfiduria (MCDU). Alternatively spliced transcript variants encoding same or different isoforms have been identified for this gene. [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=-0.92).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MPST | NM_021126.8 | c.656-226G>A | intron_variant | ENST00000429360.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPST | ENST00000429360.6 | c.656-226G>A | intron_variant | 1 | NM_021126.8 |
Frequencies
GnomAD3 genomes ? AF: 0.491 AC: 74554AN: 151876Hom.: 20987 Cov.: 32
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GnomAD4 exome AF: 0.407 AC: 159877AN: 392606Hom.: 35236 Cov.: 4 AF XY: 0.404 AC XY: 82938AN XY: 205054
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GnomAD4 genome ? AF: 0.491 AC: 74644AN: 151994Hom.: 21030 Cov.: 32 AF XY: 0.489 AC XY: 36330AN XY: 74266
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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