chr9-98293840-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_005458.8(GABBR2):c.2605A>C(p.Thr869Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,126 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T869A) has been classified as Benign.
Frequency
Consequence
NM_005458.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABBR2 | NM_005458.8 | c.2605A>C | p.Thr869Pro | missense_variant | 18/19 | ENST00000259455.4 | |
GABBR2 | XM_017015331.3 | c.2311A>C | p.Thr771Pro | missense_variant | 17/18 | ||
GABBR2 | XM_005252316.6 | c.1831A>C | p.Thr611Pro | missense_variant | 16/17 | ||
GABBR2 | XM_017015332.3 | c.1831A>C | p.Thr611Pro | missense_variant | 15/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABBR2 | ENST00000259455.4 | c.2605A>C | p.Thr869Pro | missense_variant | 18/19 | 1 | NM_005458.8 | P1 | |
GABBR2 | ENST00000637410.1 | n.2383A>C | non_coding_transcript_exon_variant | 18/19 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460126Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 726520
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at