rs11568816
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000671.4(ADH5):c.-72C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000378 in 1,368,748 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00027 ( 0 hom., cov: 29)
Exomes 𝑓: 0.00039 ( 0 hom. )
Consequence
ADH5
NM_000671.4 5_prime_UTR
NM_000671.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.475
Genes affected
ADH5 (HGNC:253): (alcohol dehydrogenase 5 (class III), chi polypeptide) This gene encodes 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 encoded protein forms a homodimer. It has virtually no activity for ethanol oxidation, but exhibits high activity for oxidation of long-chain primary alcohols and for oxidation of S-hydroxymethyl-glutathione, a spontaneous adduct between formaldehyde and glutathione. This enzyme is an important component of cellular metabolism for the elimination of formaldehyde, a potent irritant and sensitizing agent that causes lacrymation, rhinitis, pharyngitis, and contact dermatitis. The human genome contains several non-transcribed pseudogenes related to this gene. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADH5 | NM_000671.4 | c.-72C>T | 5_prime_UTR_variant | 1/9 | ENST00000296412.14 | NP_000662.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADH5 | ENST00000296412.14 | c.-72C>T | 5_prime_UTR_variant | 1/9 | 1 | NM_000671.4 | ENSP00000296412.8 |
Frequencies
GnomAD3 genomes AF: 0.000272 AC: 40AN: 147322Hom.: 0 Cov.: 29
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GnomAD4 exome AF: 0.000391 AC: 478AN: 1221320Hom.: 0 Cov.: 19 AF XY: 0.000374 AC XY: 228AN XY: 610110
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GnomAD4 genome AF: 0.000271 AC: 40AN: 147428Hom.: 0 Cov.: 29 AF XY: 0.000153 AC XY: 11AN XY: 71732
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at