chr4-46250306-A-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_000807.4(GABRA2):c.*2T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00235 in 1,606,202 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_000807.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GABRA2 | NM_000807.4 | c.*2T>A | 3_prime_UTR_variant | Exon 10 of 10 | ENST00000381620.9 | NP_000798.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0123 AC: 1858AN: 151626Hom.: 41 Cov.: 32
GnomAD3 exomes AF: 0.00313 AC: 771AN: 246274Hom.: 11 AF XY: 0.00225 AC XY: 300AN XY: 133350
GnomAD4 exome AF: 0.00131 AC: 1899AN: 1454458Hom.: 36 Cov.: 30 AF XY: 0.00110 AC XY: 795AN XY: 723374
GnomAD4 genome AF: 0.0124 AC: 1882AN: 151744Hom.: 43 Cov.: 32 AF XY: 0.0123 AC XY: 909AN XY: 74154
ClinVar
Submissions by phenotype
GABRA2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at