rs4147539
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_000668.6(ADH1B):c.260-23_260-21del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0905 in 1,605,764 control chromosomes in the GnomAD database, including 8,919 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.096 ( 1008 hom., cov: 31)
Exomes 𝑓: 0.090 ( 7911 hom. )
Consequence
ADH1B
NM_000668.6 intron
NM_000668.6 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.447
Genes affected
ADH1B (HGNC:250): (alcohol dehydrogenase 1B (class I), beta polypeptide) The protein encoded by this gene is a member of the alcohol dehydrogenase family. Members of this enzyme family metabolize a wide variety of substrates, including ethanol, retinol, other aliphatic alcohols, hydroxysteroids, and lipid peroxidation products. This encoded protein, consisting of several homo- and heterodimers of alpha, beta, and gamma subunits, exhibits high activity for ethanol oxidation and plays a major role in ethanol catabolism. Three genes encoding alpha, beta and gamma subunits are tandemly organized in a genomic segment as a gene cluster. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADH1B | NM_000668.6 | c.260-23_260-21del | intron_variant | ENST00000305046.13 | |||
ADH1B | NM_001286650.2 | c.140-23_140-21del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADH1B | ENST00000305046.13 | c.260-23_260-21del | intron_variant | 1 | NM_000668.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0955 AC: 14529AN: 152130Hom.: 1001 Cov.: 31
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GnomAD3 exomes AF: 0.119 AC: 29615AN: 249342Hom.: 3129 AF XY: 0.107 AC XY: 14437AN XY: 135004
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GnomAD4 exome AF: 0.0900 AC: 130748AN: 1453516Hom.: 7911 AF XY: 0.0876 AC XY: 63386AN XY: 723572
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GnomAD4 genome AF: 0.0956 AC: 14553AN: 152248Hom.: 1008 Cov.: 31 AF XY: 0.100 AC XY: 7478AN XY: 74440
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ClinVar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at