rs6426611
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003748.4(ALDH4A1):c.678+75T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.994 in 1,593,238 control chromosomes in the GnomAD database, including 787,985 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.97 ( 71835 hom., cov: 34)
Exomes 𝑓: 1.0 ( 716150 hom. )
Consequence
ALDH4A1
NM_003748.4 intron
NM_003748.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.87
Genes affected
ALDH4A1 (HGNC:406): (aldehyde dehydrogenase 4 family member A1) This protein belongs to the aldehyde dehydrogenase family of proteins. This enzyme is a mitochondrial matrix NAD-dependent dehydrogenase which catalyzes the second step of the proline degradation pathway, converting pyrroline-5-carboxylate to glutamate. Deficiency of this enzyme is associated with type II hyperprolinemia, an autosomal recessive disorder characterized by accumulation of delta-1-pyrroline-5-carboxylate (P5C) and proline. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jun 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
?
Variant 1-18883049-A-G is Benign according to our data. Variant chr1-18883049-A-G is described in ClinVar as [Benign]. Clinvar id is 1188911.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH4A1 | NM_003748.4 | c.678+75T>C | intron_variant | ENST00000375341.8 | |||
ALDH4A1 | NM_001161504.2 | c.498+75T>C | intron_variant | ||||
ALDH4A1 | NM_001319218.2 | c.678+75T>C | intron_variant | ||||
ALDH4A1 | NM_170726.3 | c.678+75T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH4A1 | ENST00000375341.8 | c.678+75T>C | intron_variant | 1 | NM_003748.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.970 AC: 147693AN: 152232Hom.: 71804 Cov.: 34
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GnomAD4 exome AF: 0.997 AC: 1436394AN: 1440888Hom.: 716150 AF XY: 0.997 AC XY: 716173AN XY: 718102
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GnomAD4 genome ? AF: 0.970 AC: 147779AN: 152350Hom.: 71835 Cov.: 34 AF XY: 0.970 AC XY: 72283AN XY: 74486
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hyperprolinemia type 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational scores
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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