chr4-46928613-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.1277G>A(p.Arg426Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,613,548 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.1277G>A | p.Arg426Gln | missense_variant | 9/9 | ENST00000264318.4 | |
GABRA4 | NM_001204266.2 | c.1220G>A | p.Arg407Gln | missense_variant | 9/9 | ||
GABRA4 | NM_001204267.2 | c.1067G>A | p.Arg356Gln | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRA4 | ENST00000264318.4 | c.1277G>A | p.Arg426Gln | missense_variant | 9/9 | 1 | NM_000809.4 | P1 | |
GABRA4 | ENST00000508560.5 | c.*1098G>A | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 3 | ||||
GABRA4 | ENST00000511523.5 | c.*945G>A | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152026Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251082Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135672
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461522Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727054
GnomAD4 genome AF: 0.000105 AC: 16AN: 152026Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74246
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 06, 2022 | 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