rs368427726
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001182.5(ALDH7A1):c.63T>C(p.Pro21=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000157 in 1,567,558 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P21P) 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH7A1 | NM_001182.5 | c.63T>C | p.Pro21= | synonymous_variant | 1/18 | ENST00000409134.8 | |
ALDH7A1 | NM_001202404.2 | c.63T>C | p.Pro21= | synonymous_variant | 1/16 | ||
ALDH7A1 | NM_001201377.2 | c.-22T>C | 5_prime_UTR_variant | 1/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH7A1 | ENST00000409134.8 | c.63T>C | p.Pro21= | synonymous_variant | 1/18 | 1 | NM_001182.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152204Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000143 AC: 25AN: 175394Hom.: 0 AF XY: 0.000118 AC XY: 11AN XY: 93538
GnomAD4 exome AF: 0.000160 AC: 226AN: 1415354Hom.: 0 Cov.: 32 AF XY: 0.000169 AC XY: 118AN XY: 699898
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152204Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74358
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2022 | ALDH7A1: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 19, 2016 | - - |
Pyridoxine-dependent epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at