chr4-46965041-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000809.4(GABRA4):āc.1063A>Gā(p.Thr355Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0032 in 1,612,096 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_000809.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRA4 | NM_000809.4 | c.1063A>G | p.Thr355Ala | missense_variant | 8/9 | ENST00000264318.4 | |
GABRA4 | NM_001204266.2 | c.1006A>G | p.Thr336Ala | missense_variant | 8/9 | ||
GABRA4 | NM_001204267.2 | c.853A>G | p.Thr285Ala | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRA4 | ENST00000264318.4 | c.1063A>G | p.Thr355Ala | missense_variant | 8/9 | 1 | NM_000809.4 | P1 | |
GABRA4 | ENST00000508560.5 | c.*884A>G | 3_prime_UTR_variant, NMD_transcript_variant | 8/9 | 3 | ||||
GABRA4 | ENST00000511523.5 | c.*731A>G | 3_prime_UTR_variant, NMD_transcript_variant | 7/8 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00190 AC: 289AN: 151746Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00159 AC: 397AN: 250466Hom.: 0 AF XY: 0.00158 AC XY: 214AN XY: 135376
GnomAD4 exome AF: 0.00333 AC: 4868AN: 1460232Hom.: 10 Cov.: 31 AF XY: 0.00315 AC XY: 2289AN XY: 726408
GnomAD4 genome AF: 0.00190 AC: 289AN: 151864Hom.: 0 Cov.: 33 AF XY: 0.00168 AC XY: 125AN XY: 74224
ClinVar
Submissions by phenotype
GABRA4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 02, 2023 | This variant is classified as likely 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