rs9652369
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_005589.4(ALDH6A1):c.1503+1865A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00542 in 152,106 control chromosomes in the GnomAD database, including 9 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 0.0054 ( 9 hom., cov: 31)
Consequence
ALDH6A1
NM_005589.4 intron
NM_005589.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.301
Genes affected
ALDH6A1 (HGNC:7179): (aldehyde dehydrogenase 6 family member A1) This gene encodes a member of the aldehyde dehydrogenase protein family. The encoded protein is a mitochondrial methylmalonate semialdehyde dehydrogenase that plays a role in the valine and pyrimidine catabolic pathways. This protein catalyzes the irreversible oxidative decarboxylation of malonate and methylmalonate semialdehydes to acetyl- and propionyl-CoA. Methylmalonate semialdehyde dehydrogenase deficiency is characterized by elevated beta-alanine, 3-hydroxypropionic acid, and both isomers of 3-amino and 3-hydroxyisobutyric acids in urine organic acids. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jun 2013]
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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=-0.8).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00542 (825/152106) while in subpopulation AFR AF= 0.0193 (800/41490). AF 95% confidence interval is 0.0182. There are 9 homozygotes in gnomad4. There are 381 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH6A1 | NM_005589.4 | c.1503+1865A>T | intron_variant | ENST00000553458.6 | |||
BBOF1 | NM_025057.3 | c.1579-1731T>A | intron_variant | ENST00000394009.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BBOF1 | ENST00000394009.5 | c.1579-1731T>A | intron_variant | 2 | NM_025057.3 | P1 | |||
ALDH6A1 | ENST00000553458.6 | c.1503+1865A>T | intron_variant | 1 | NM_005589.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00535 AC: 813AN: 151988Hom.: 7 Cov.: 31
GnomAD3 genomes
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GnomAD4 genome ? AF: 0.00542 AC: 825AN: 152106Hom.: 9 Cov.: 31 AF XY: 0.00513 AC XY: 381AN XY: 74340
GnomAD4 genome
?
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152106
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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