5-126593396-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001182.5(ALDH7A1):c.201G>A(p.Thr67=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,461,636 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T67T) has been classified as Likely benign.
Frequency
Consequence
NM_001182.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH7A1 | NM_001182.5 | c.201G>A | p.Thr67= | synonymous_variant | 2/18 | ENST00000409134.8 | |
ALDH7A1 | NM_001201377.2 | c.117G>A | p.Thr39= | synonymous_variant | 2/18 | ||
ALDH7A1 | NM_001202404.2 | c.201G>A | p.Thr67= | synonymous_variant | 2/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH7A1 | ENST00000409134.8 | c.201G>A | p.Thr67= | synonymous_variant | 2/18 | 1 | NM_001182.5 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251358Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135876
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461636Hom.: 0 Cov.: 34 AF XY: 0.0000138 AC XY: 10AN XY: 727122
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Pyridoxine-dependent epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at