chr4-46928488-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_000809.4(GABRA4):āc.1402G>Cā(p.Ala468Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,472 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_000809.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRA4 | NM_000809.4 | c.1402G>C | p.Ala468Pro | missense_variant | 9/9 | ENST00000264318.4 | |
GABRA4 | NM_001204266.2 | c.1345G>C | p.Ala449Pro | missense_variant | 9/9 | ||
GABRA4 | NM_001204267.2 | c.1192G>C | p.Ala398Pro | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRA4 | ENST00000264318.4 | c.1402G>C | p.Ala468Pro | missense_variant | 9/9 | 1 | NM_000809.4 | P1 | |
GABRA4 | ENST00000508560.5 | c.*1223G>C | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 3 | ||||
GABRA4 | ENST00000511523.5 | c.*1070G>C | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152036Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250930Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135616
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461436Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727016
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152036Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74264
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2022 | The c.1402G>C (p.A468P) alteration is located in exon 9 (coding exon 9) of the GABRA4 gene. This alteration results from a G to C substitution at nucleotide position 1402, causing the alanine (A) at amino acid position 468 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at