rs1573496
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM1BP4_StrongBA1
The NM_000673.7(ADH7):āc.239G>Cā(p.Gly80Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0924 in 1,613,220 control chromosomes in the GnomAD database, including 8,053 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: š 0.077 ( 662 hom., cov: 32)
Exomes š: 0.094 ( 7391 hom. )
Consequence
ADH7
NM_000673.7 missense
NM_000673.7 missense
Scores
2
6
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.81
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 -10 ACMG points.
PM1
?
In a binding_site (size 0) in uniprot entity ADH7_HUMAN
BP4
?
Computational evidence support a benign effect (MetaRNN=0.002137661).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADH7 | NM_000673.7 | c.239G>C | p.Gly80Ala | missense_variant | 3/9 | ENST00000437033.7 | |
ADH7 | NM_001166504.2 | c.299G>C | p.Gly100Ala | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADH7 | ENST00000437033.7 | c.239G>C | p.Gly80Ala | missense_variant | 3/9 | 1 | NM_000673.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0771 AC: 11715AN: 152012Hom.: 663 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0855 AC: 21398AN: 250368Hom.: 1211 AF XY: 0.0876 AC XY: 11852AN XY: 135236
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GnomAD4 exome AF: 0.0939 AC: 137267AN: 1461090Hom.: 7391 Cov.: 32 AF XY: 0.0938 AC XY: 68160AN XY: 726762
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GnomAD4 genome ? AF: 0.0770 AC: 11714AN: 152130Hom.: 662 Cov.: 32 AF XY: 0.0783 AC XY: 5824AN XY: 74372
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352
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358
ESP6500AA
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80
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950
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10184
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.;.;.
MutationTaster
Benign
P;P;P;P
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D;D;D;D
REVEL
Benign
Sift
Pathogenic
D;D;D;D;D
Sift4G
Uncertain
D;D;D;D;.
Polyphen
D;.;.;.;.
Vest4
MPC
0.049
ClinPred
T
GERP RS
Varity_R
gMVP
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