rs3857224
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001102470.2(ADH6):c.828+140G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 919,136 control chromosomes in the GnomAD database, including 73,068 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 0.42 ( 14934 hom., cov: 32)
Exomes 𝑓: 0.36 ( 58134 hom. )
Consequence
ADH6
NM_001102470.2 intron
NM_001102470.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00900
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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADH6 | NM_001102470.2 | c.828+140G>A | intron_variant | ENST00000394899.6 | NP_001095940.1 | |||
ADH6 | NM_000672.4 | c.828+140G>A | intron_variant | NP_000663.1 | ||||
LOC100507053 | NR_037884.1 | n.3789+4097C>T | intron_variant | |||||
ADH6 | NR_132990.2 | n.563+140G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADH6 | ENST00000394899.6 | c.828+140G>A | intron_variant | 2 | NM_001102470.2 | ENSP00000378359.2 |
Frequencies
GnomAD3 genomes AF: 0.422 AC: 64037AN: 151748Hom.: 14918 Cov.: 32
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GnomAD4 exome AF: 0.364 AC: 279555AN: 767270Hom.: 58134 Cov.: 10 AF XY: 0.367 AC XY: 143636AN XY: 391236
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GnomAD4 genome AF: 0.422 AC: 64094AN: 151866Hom.: 14934 Cov.: 32 AF XY: 0.425 AC XY: 31539AN XY: 74228
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at