rs894369
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000673.7(ADH7):c.*459G>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 0.775 in 152,378 control chromosomes in the GnomAD database, including 46,285 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 0.78 ( 46183 hom., cov: 32)
Exomes 𝑓: 0.78 ( 102 hom. )
Consequence
ADH7
NM_000673.7 3_prime_UTR
NM_000673.7 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.216
Genes affected
ADH7 (HGNC:256): (alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide) This gene encodes class IV alcohol dehydrogenase 7 mu or sigma subunit, which is a member of the alcohol dehydrogenase family. Members of this family metabolize a wide variety of substrates, including ethanol, retinol, other aliphatic alcohols, hydroxysteroids, and lipid peroxidation products. The enzyme encoded by this gene is inefficient in ethanol oxidation, but is the most active as a retinol dehydrogenase; thus it may participate in the synthesis of retinoic acid, a hormone important for cellular differentiation. The expression of this gene is much more abundant in stomach than liver, thus differing from the other known gene family members. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADH7 | NM_000673.7 | c.*459G>C | 3_prime_UTR_variant | 9/9 | ENST00000437033.7 | ||
ADH7 | NM_001166504.2 | c.*459G>C | 3_prime_UTR_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADH7 | ENST00000437033.7 | c.*459G>C | 3_prime_UTR_variant | 9/9 | 1 | NM_000673.7 | P1 | ||
ADH7 | ENST00000209665.8 | c.*459G>C | 3_prime_UTR_variant | 9/9 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.775 AC: 117813AN: 151926Hom.: 46148 Cov.: 32
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GnomAD4 exome AF: 0.778 AC: 260AN: 334Hom.: 102 Cov.: 0 AF XY: 0.766 AC XY: 144AN XY: 188
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GnomAD4 genome ? AF: 0.775 AC: 117900AN: 152044Hom.: 46183 Cov.: 32 AF XY: 0.769 AC XY: 57159AN XY: 74294
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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