9-98290593-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_005458.8(GABBR2):c.2817G>C(p.Ser939=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000207 in 1,398,160 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S939S) has been classified as Likely benign.
Frequency
Consequence
NM_005458.8 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABBR2 | NM_005458.8 | c.2817G>C | p.Ser939= | synonymous_variant | 19/19 | ENST00000259455.4 | |
GABBR2 | XM_017015331.3 | c.2523G>C | p.Ser841= | synonymous_variant | 18/18 | ||
GABBR2 | XM_005252316.6 | c.2043G>C | p.Ser681= | synonymous_variant | 17/17 | ||
GABBR2 | XM_017015332.3 | c.2043G>C | p.Ser681= | synonymous_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABBR2 | ENST00000259455.4 | c.2817G>C | p.Ser939= | synonymous_variant | 19/19 | 1 | NM_005458.8 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000194 AC: 2AN: 102890Hom.: 0 AF XY: 0.0000359 AC XY: 2AN XY: 55722
GnomAD4 exome AF: 0.0000225 AC: 28AN: 1246026Hom.: 0 Cov.: 31 AF XY: 0.0000282 AC XY: 17AN XY: 603832
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74316
ClinVar
Submissions by phenotype
Epileptic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at