rs1055271
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017584.6(MIOX):c.*55G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 1,534,558 control chromosomes in the GnomAD database, including 88,026 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 0.27 ( 6423 hom., cov: 34)
Exomes 𝑓: 0.34 ( 81603 hom. )
Consequence
MIOX
NM_017584.6 3_prime_UTR
NM_017584.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.60
Genes affected
MIOX (HGNC:14522): (myo-inositol oxygenase) Enables ferric iron binding activity and inositol oxygenase activity. Involved in inositol catabolic process. Predicted to be located in cytoplasm and inclusion body. [provided by Alliance of Genome Resources, Apr 2022]
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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 (NFE) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIOX | NM_017584.6 | c.*55G>C | 3_prime_UTR_variant | 10/10 | ENST00000216075.11 | ||
MIOX | XM_005261925.5 | c.*55G>C | 3_prime_UTR_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIOX | ENST00000216075.11 | c.*55G>C | 3_prime_UTR_variant | 10/10 | 1 | NM_017584.6 | P1 | ||
MIOX | ENST00000395732.7 | c.*86G>C | 3_prime_UTR_variant | 10/10 | 1 | ||||
MIOX | ENST00000395733.7 | c.*86G>C | 3_prime_UTR_variant | 8/8 | 1 | ||||
MIOX | ENST00000451761.1 | c.*55G>C | 3_prime_UTR_variant | 9/9 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.270 AC: 40990AN: 152090Hom.: 6423 Cov.: 34
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GnomAD4 exome AF: 0.339 AC: 469258AN: 1382350Hom.: 81603 Cov.: 22 AF XY: 0.337 AC XY: 232940AN XY: 691304
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GnomAD4 genome ? AF: 0.269 AC: 40990AN: 152208Hom.: 6423 Cov.: 34 AF XY: 0.264 AC XY: 19650AN XY: 74404
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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