rs971074
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_000673.7(ADH7):c.654G>A(p.Arg218=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,613,624 control chromosomes in the GnomAD database, including 11,731 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 0.13 ( 1435 hom., cov: 32)
Exomes 𝑓: 0.12 ( 10296 hom. )
Consequence
ADH7
NM_000673.7 synonymous
NM_000673.7 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.672
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP7
?
Synonymous conserved (PhyloP=0.672 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADH7 | NM_000673.7 | c.654G>A | p.Arg218= | synonymous_variant | 6/9 | ENST00000437033.7 | |
ADH7 | NM_001166504.2 | c.714G>A | p.Arg238= | synonymous_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADH7 | ENST00000437033.7 | c.654G>A | p.Arg218= | synonymous_variant | 6/9 | 1 | NM_000673.7 | P1 | |
ADH7 | ENST00000209665.8 | c.690G>A | p.Arg230= | synonymous_variant | 6/9 | 1 | |||
ADH7 | ENST00000476959.5 | c.714G>A | p.Arg238= | synonymous_variant | 6/9 | 2 | |||
ADH7 | ENST00000482593.5 | c.483G>A | p.Arg161= | synonymous_variant | 7/10 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.133 AC: 20202AN: 151930Hom.: 1430 Cov.: 32
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GnomAD3 exomes AF: 0.121 AC: 30480AN: 251046Hom.: 1986 AF XY: 0.120 AC XY: 16271AN XY: 135652
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GnomAD4 exome AF: 0.115 AC: 168798AN: 1461576Hom.: 10296 Cov.: 33 AF XY: 0.115 AC XY: 83807AN XY: 727090
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GnomAD4 genome ? AF: 0.133 AC: 20245AN: 152048Hom.: 1435 Cov.: 32 AF XY: 0.134 AC XY: 9945AN XY: 74318
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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