5-162102625-G-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The ENST00000414552.6(GABRG2):c.703G>T(p.Gly235Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 453,378 control chromosomes in the GnomAD database, including 2,565 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. G235G) has been classified as Benign.
Frequency
Consequence
ENST00000414552.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRG2 | NM_198904.4 | c.632-1264G>T | intron_variant | ENST00000639213.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRG2 | ENST00000639213.2 | c.632-1264G>T | intron_variant | 1 | NM_198904.4 | A1 |
Frequencies
GnomAD3 genomes AF: 0.107 AC: 16230AN: 151778Hom.: 912 Cov.: 32
GnomAD3 exomes AF: 0.0969 AC: 12418AN: 128194Hom.: 639 AF XY: 0.0983 AC XY: 6897AN XY: 70192
GnomAD4 exome AF: 0.101 AC: 30468AN: 301482Hom.: 1653 Cov.: 0 AF XY: 0.102 AC XY: 17545AN XY: 171808
GnomAD4 genome AF: 0.107 AC: 16237AN: 151896Hom.: 912 Cov.: 32 AF XY: 0.106 AC XY: 7892AN XY: 74198
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 14, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at