rs1126672
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_000670.5(ADH4):c.1051C>T(p.Leu351=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 1,610,126 control chromosomes in the GnomAD database, including 53,540 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 0.21 ( 4047 hom., cov: 32)
Exomes 𝑓: 0.25 ( 49493 hom. )
Consequence
ADH4
NM_000670.5 synonymous
NM_000670.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0210
Genes affected
ADH4 (HGNC:252): (alcohol dehydrogenase 4 (class II), pi polypeptide) This gene encodes class II alcohol dehydrogenase 4 pi subunit, which is a member of the alcohol dehydrogenase family. Members of this enzyme family metabolize a wide variety of substrates, including ethanol, retinol, other aliphatic alcohols, hydroxysteroids, and lipid peroxidation products. Class II alcohol dehydrogenase is a homodimer composed of 2 pi subunits. It exhibits a high activity for oxidation of long-chain aliphatic alcohols and aromatic alcohols and is less sensitive to pyrazole. This gene is localized to chromosome 4 in the cluster of alcohol dehydrogenase genes. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP7
Synonymous conserved (PhyloP=0.021 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADH4 | NM_000670.5 | c.1051C>T | p.Leu351= | synonymous_variant | 8/9 | ENST00000265512.12 | NP_000661.2 | |
LOC100507053 | NR_037884.1 | n.429-6894G>A | intron_variant, non_coding_transcript_variant | |||||
ADH4 | NM_001306171.2 | c.1108C>T | p.Leu370= | synonymous_variant | 9/10 | NP_001293100.1 | ||
ADH4 | NM_001306172.2 | c.1108C>T | p.Leu370= | synonymous_variant | 9/10 | NP_001293101.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADH4 | ENST00000265512.12 | c.1051C>T | p.Leu351= | synonymous_variant | 8/9 | 1 | NM_000670.5 | ENSP00000265512 | P1 | |
ENST00000500358.6 | n.429-6894G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.211 AC: 32040AN: 152042Hom.: 4050 Cov.: 32
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GnomAD3 exomes AF: 0.208 AC: 52179AN: 251012Hom.: 6683 AF XY: 0.214 AC XY: 28968AN XY: 135644
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GnomAD4 exome AF: 0.251 AC: 365928AN: 1457966Hom.: 49493 Cov.: 32 AF XY: 0.249 AC XY: 180803AN XY: 725252
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GnomAD4 genome AF: 0.211 AC: 32041AN: 152160Hom.: 4047 Cov.: 32 AF XY: 0.203 AC XY: 15096AN XY: 74366
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ClinVar
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