rs4784708
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005951.2(MT1H):c.28+90G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0514 in 1,562,122 control chromosomes in the GnomAD database, including 2,399 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 0.037 ( 138 hom., cov: 33)
Exomes 𝑓: 0.053 ( 2261 hom. )
Consequence
MT1H
NM_005951.2 intron
NM_005951.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.50
Genes affected
MT1H (HGNC:7400): (metallothionein 1H) Predicted to enable zinc ion binding activity. Involved in cellular response to cadmium ion and cellular response to zinc ion. Predicted to be active in cytoplasm and nucleus. [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=-0.84).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0558 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MT1H | NM_005951.2 | c.28+90G>C | intron_variant | ENST00000332374.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT1H | ENST00000332374.5 | c.28+90G>C | intron_variant | 1 | NM_005951.2 | P1 | |||
MT1H | ENST00000569155.1 | c.28+90G>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0372 AC: 5662AN: 152110Hom.: 138 Cov.: 33
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GnomAD4 exome AF: 0.0529 AC: 74650AN: 1409894Hom.: 2261 AF XY: 0.0521 AC XY: 36658AN XY: 703806
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GnomAD4 genome ? AF: 0.0372 AC: 5662AN: 152228Hom.: 138 Cov.: 33 AF XY: 0.0364 AC XY: 2712AN XY: 74434
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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