chr5-126542500-C-CA
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001182.5(ALDH7A1):c.*2464_*2465insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 150,644 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.056 ( 0 hom. )
Consequence
ALDH7A1
NM_001182.5 3_prime_UTR
NM_001182.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.291
Genes affected
ALDH7A1 (HGNC:877): (aldehyde dehydrogenase 7 family member A1) The protein encoded by this gene is a member of subfamily 7 in the aldehyde dehydrogenase gene family. These enzymes are thought to play a major role in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. This particular member has homology to a previously described protein from the green garden pea, the 26g pea turgor protein. It is also involved in lysine catabolism that is known to occur in the mitochondrial matrix. Recent reports show that this protein is found both in the cytosol and the mitochondria, and the two forms likely arise from the use of alternative translation initiation sites. An additional variant encoding a different isoform has also been found for this gene. Mutations in this gene are associated with pyridoxine-dependent epilepsy. Several related pseudogenes have also been identified. [provided by RefSeq, Jan 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAdExome4 highest subpopulation (NFE) allele frequency = 0.0714 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALDH7A1 | NM_001182.5 | c.*2464_*2465insT | 3_prime_UTR_variant | 18/18 | ENST00000409134.8 | NP_001173.2 | ||
ALDH7A1 | NM_001201377.2 | c.*2464_*2465insT | 3_prime_UTR_variant | 18/18 | NP_001188306.1 | |||
ALDH7A1 | NM_001202404.2 | c.*2464_*2465insT | 3_prime_UTR_variant | 16/16 | NP_001189333.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALDH7A1 | ENST00000409134.8 | c.*2464_*2465insT | 3_prime_UTR_variant | 18/18 | 1 | NM_001182.5 | ENSP00000387123 | P4 | ||
ALDH7A1 | ENST00000635851.1 | c.1564-1513_1564-1512insT | intron_variant | 5 | ENSP00000490819 | |||||
ALDH7A1 | ENST00000637782.1 | c.1565+3823_1565+3824insT | intron_variant | 5 | ENSP00000490024 |
Frequencies
GnomAD3 genomes AF: 0.0000997 AC: 15AN: 150512Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0556 AC: 1AN: 18Hom.: 0 Cov.: 0 AF XY: 0.0556 AC XY: 1AN XY: 18
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GnomAD4 genome AF: 0.000106 AC: 16AN: 150626Hom.: 0 Cov.: 32 AF XY: 0.0000817 AC XY: 6AN XY: 73470
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Pyridoxine-dependent epilepsy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at