NM_001127644.2:c.-243A>G
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001127644.2(GABRA1):c.-243A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,052 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 (★).
Frequency
Consequence
NM_001127644.2 5_prime_UTR
Scores
Clinical Significance
Conservation
Publications
- developmental and epileptic encephalopathy, 19Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
- genetic developmental and epileptic encephalopathyInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- epilepsy, idiopathic generalized, susceptibility to, 13Inheritance: AD Classification: STRONG Submitted by: G2P
- Dravet syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- juvenile myoclonic epilepsyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GABRA1 | NM_001127644.2 | c.-243A>G | 5_prime_UTR_variant | Exon 1 of 10 | ENST00000393943.10 | NP_001121116.1 | ||
GABRA1 | NM_000806.5 | c.-243A>G | 5_prime_UTR_variant | Exon 2 of 11 | NP_000797.2 | |||
GABRA1 | NM_001127643.2 | c.-243A>G | 5_prime_UTR_variant | Exon 2 of 11 | NP_001121115.1 | |||
LOC105377696 | XR_941158.4 | n.74+2325T>C | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 31 show subpopulations
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 90Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 58
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74272 show subpopulations
ClinVar
Submissions by phenotype
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