rs8187999
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000689.5(ALDH1A1):c.*315G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0202 in 204,484 control chromosomes in the GnomAD database, including 54 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 0.019 ( 36 hom., cov: 32)
Exomes 𝑓: 0.024 ( 18 hom. )
Consequence
ALDH1A1
NM_000689.5 3_prime_UTR
NM_000689.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0340
Genes affected
ALDH1A1 (HGNC:402): (aldehyde dehydrogenase 1 family member A1) The protein encoded by this gene belongs to the aldehyde dehydrogenase family. Aldehyde dehydrogenase is the next enzyme after alcohol dehydrogenase in the major pathway of alcohol metabolism. There are two major aldehyde dehydrogenase isozymes in the liver, cytosolic and mitochondrial, which are encoded by distinct genes, and can be distinguished by their electrophoretic mobility, kinetic properties, and subcellular localization. This gene encodes the cytosolic isozyme. Studies in mice show that through its role in retinol metabolism, this gene may also be involved in the regulation of the metabolic responses to high-fat diet. [provided by RefSeq, Mar 2011]
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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=-0.65).
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0191 (2901/152102) while in subpopulation SAS AF= 0.0332 (160/4818). AF 95% confidence interval is 0.029. There are 36 homozygotes in gnomad4. There are 1457 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 2901 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH1A1 | NM_000689.5 | c.*315G>C | 3_prime_UTR_variant | 13/13 | ENST00000297785.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH1A1 | ENST00000297785.8 | c.*315G>C | 3_prime_UTR_variant | 13/13 | 1 | NM_000689.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0191 AC: 2903AN: 151984Hom.: 36 Cov.: 32
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GnomAD4 exome AF: 0.0237 AC: 1239AN: 52382Hom.: 18 Cov.: 0 AF XY: 0.0234 AC XY: 640AN XY: 27392
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GnomAD4 genome ? AF: 0.0191 AC: 2901AN: 152102Hom.: 36 Cov.: 32 AF XY: 0.0196 AC XY: 1457AN XY: 74340
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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