rs2286164
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000694.4(ALDH3B1):c.1117-29A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,499,684 control chromosomes in the GnomAD database, including 41,766 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 0.26 ( 5658 hom., cov: 31)
Exomes 𝑓: 0.23 ( 36108 hom. )
Consequence
ALDH3B1
NM_000694.4 intron
NM_000694.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.84
Genes affected
ALDH3B1 (HGNC:410): (aldehyde dehydrogenase 3 family member B1) This gene encodes a member of the aldehyde dehydrogenase protein family. Aldehyde dehydrogenases are a family of isozymes that may play a major role in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. The encoded protein is able to oxidize long-chain fatty aldehydes in vitro, and may play a role in protection from oxidative stress. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
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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=-0.95).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH3B1 | NM_000694.4 | c.1117-29A>G | intron_variant | ENST00000342456.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH3B1 | ENST00000342456.11 | c.1117-29A>G | intron_variant | 1 | NM_000694.4 | P1 | |||
ENST00000532296.1 | n.341-648T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.261 AC: 39595AN: 151850Hom.: 5652 Cov.: 31
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GnomAD3 exomes AF: 0.211 AC: 34893AN: 165030Hom.: 4061 AF XY: 0.214 AC XY: 18965AN XY: 88640
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GnomAD4 exome AF: 0.228 AC: 306918AN: 1347716Hom.: 36108 Cov.: 21 AF XY: 0.228 AC XY: 151420AN XY: 664458
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GnomAD4 genome ? AF: 0.261 AC: 39624AN: 151968Hom.: 5658 Cov.: 31 AF XY: 0.253 AC XY: 18812AN XY: 74294
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at