rs2000864
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000500358.6(ENSG00000246090):n.3715-1738C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 396,300 control chromosomes in the GnomAD database, including 63,587 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 0.56 ( 24730 hom., cov: 32)
Exomes 𝑓: 0.55 ( 38857 hom. )
Consequence
ENSG00000246090
ENST00000500358.6 intron
ENST00000500358.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.398
Genes affected
ADH6 (HGNC:255): (alcohol dehydrogenase 6 (class V)) This gene encodes class V alcohol dehydrogenase, 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. This gene is expressed in the stomach as well as in the liver, and it contains a glucocorticoid response element upstream of its 5' UTR, which is a steroid hormone receptor binding site. Alternatively spliced transcript variants encoding different isoforms have been found 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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC100507053 | NR_037884.1 | n.3715-1738C>A | intron_variant | |||||
ADH6 | NM_001102470.2 | c.*1600G>T | downstream_gene_variant | ENST00000394899.6 | NP_001095940.1 | |||
ADH6 | NM_000672.4 | c.*2302G>T | downstream_gene_variant | NP_000663.1 | ||||
ADH6 | NR_132990.2 | n.*20G>T | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADH6 | ENST00000394899.6 | c.*1600G>T | downstream_gene_variant | 2 | NM_001102470.2 | ENSP00000378359.2 |
Frequencies
GnomAD3 genomes AF: 0.563 AC: 85451AN: 151868Hom.: 24707 Cov.: 32
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GnomAD4 exome AF: 0.549 AC: 134226AN: 244316Hom.: 38857 Cov.: 0 AF XY: 0.549 AC XY: 67969AN XY: 123882
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GnomAD4 genome AF: 0.563 AC: 85521AN: 151984Hom.: 24730 Cov.: 32 AF XY: 0.562 AC XY: 41785AN XY: 74286
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at