chr4-46965205-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_000809.4(GABRA4):c.899C>T(p.Thr300Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T300N) has been classified as Uncertain significance.
Frequency
Consequence
NM_000809.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRA4 | NM_000809.4 | c.899C>T | p.Thr300Ile | missense_variant | 8/9 | ENST00000264318.4 | |
GABRA4 | NM_001204266.2 | c.842C>T | p.Thr281Ile | missense_variant | 8/9 | ||
GABRA4 | NM_001204267.2 | c.689C>T | p.Thr230Ile | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRA4 | ENST00000264318.4 | c.899C>T | p.Thr300Ile | missense_variant | 8/9 | 1 | NM_000809.4 | P1 | |
GABRA4 | ENST00000508560.5 | c.*720C>T | 3_prime_UTR_variant, NMD_transcript_variant | 8/9 | 3 | ||||
GABRA4 | ENST00000511523.5 | c.*567C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/8 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1417050Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 702102
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.