rs768304032
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_005458.8(GABBR2):c.2328G>T(p.Ser776=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,792 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. S776S) has been classified as 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.2328G>T | p.Ser776= | synonymous_variant | 16/19 | ENST00000259455.4 | |
GABBR2 | XM_017015331.3 | c.2034G>T | p.Ser678= | synonymous_variant | 15/18 | ||
GABBR2 | XM_005252316.6 | c.1554G>T | p.Ser518= | synonymous_variant | 14/17 | ||
GABBR2 | XM_017015332.3 | c.1554G>T | p.Ser518= | synonymous_variant | 13/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABBR2 | ENST00000259455.4 | c.2328G>T | p.Ser776= | synonymous_variant | 16/19 | 1 | NM_005458.8 | P1 | |
GABBR2 | ENST00000636575.1 | n.10G>T | non_coding_transcript_exon_variant | 1/2 | 5 | ||||
GABBR2 | ENST00000637410.1 | n.2106G>T | non_coding_transcript_exon_variant | 16/19 | 5 | ||||
GABBR2 | ENST00000634457.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461792Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727210
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Epileptic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 06, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at