NM_001127644.2:c.-258T>C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001127644.2(GABRA1):c.-258T>C variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000243 in 152,148 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).
Frequency
Consequence
NM_001127644.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GABRA1 | NM_001127644.2 | c.-258T>C | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 10 | ENST00000393943.10 | NP_001121116.1 | ||
GABRA1 | NM_001127644.2 | c.-258T>C | 5_prime_UTR_variant | Exon 1 of 10 | ENST00000393943.10 | NP_001121116.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GABRA1 | ENST00000393943 | c.-258T>C | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 10 | 1 | NM_001127644.2 | ENSP00000377517.4 | |||
GABRA1 | ENST00000393943 | c.-258T>C | 5_prime_UTR_variant | Exon 1 of 10 | 1 | NM_001127644.2 | ENSP00000377517.4 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152030Hom.: 0 Cov.: 31
GnomAD4 exome Cov.: 0
GnomAD4 genome AF: 0.000243 AC: 37AN: 152148Hom.: 0 Cov.: 31 AF XY: 0.000282 AC XY: 21AN XY: 74382
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 19 Uncertain:1
- -
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at