rs76665287
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_005589.4(ALDH6A1):c.*2298G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ALDH6A1
NM_005589.4 3_prime_UTR
NM_005589.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.205
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 Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALDH6A1 | NM_005589.4 | c.*2298G>T | 3_prime_UTR_variant | Exon 12 of 12 | ENST00000553458.6 | NP_005580.1 | ||
BBOF1 | NM_025057.3 | c.1578+1086C>A | intron_variant | Intron 11 of 11 | ENST00000394009.5 | NP_079333.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALDH6A1 | ENST00000553458 | c.*2298G>T | 3_prime_UTR_variant | Exon 12 of 12 | 1 | NM_005589.4 | ENSP00000450436.1 | |||
BBOF1 | ENST00000394009.5 | c.1578+1086C>A | intron_variant | Intron 11 of 11 | 2 | NM_025057.3 | ENSP00000377577.3 | |||
BBOF1 | ENST00000492026.4 | n.1379+1086C>A | intron_variant | Intron 9 of 12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 140048Hom.: 0 Cov.: 31 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 58Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 32
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GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 140048Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 68232
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Data not reliable, filtered out with message: AC0;AS_VQSR
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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