chr4-46928463-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000809.4(GABRA4):c.1427G>A(p.Arg476His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,476 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
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.1427G>A | p.Arg476His | missense_variant | 9/9 | ENST00000264318.4 | |
GABRA4 | NM_001204266.2 | c.1370G>A | p.Arg457His | missense_variant | 9/9 | ||
GABRA4 | NM_001204267.2 | c.1217G>A | p.Arg406His | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRA4 | ENST00000264318.4 | c.1427G>A | p.Arg476His | missense_variant | 9/9 | 1 | NM_000809.4 | P1 | |
GABRA4 | ENST00000508560.5 | c.*1248G>A | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 3 | ||||
GABRA4 | ENST00000511523.5 | c.*1095G>A | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152000Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251084Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135696
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461476Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727038
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152000Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74244
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 06, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at