chr5-162068010-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 1P and 18B. PP2BP4_ModerateBP6_Very_StrongBS1BS2
The NM_198904.4(GABRG2):c.11C>T(p.Pro4Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,612,414 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. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_198904.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GABRG2 | NM_198904.4 | c.11C>T | p.Pro4Leu | missense_variant | 1/10 | ENST00000639213.2 | NP_944494.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GABRG2 | ENST00000639213.2 | c.11C>T | p.Pro4Leu | missense_variant | 1/10 | 1 | NM_198904.4 | ENSP00000491909 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000132 AC: 20AN: 151640Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 250926Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135584
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1460774Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726768
GnomAD4 genome AF: 0.000132 AC: 20AN: 151640Hom.: 0 Cov.: 31 AF XY: 0.0000946 AC XY: 7AN XY: 73974
ClinVar
Submissions by phenotype
GABRG2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 20, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 20, 2021 | - - |
Epilepsy, childhood absence 2;C1969810:Febrile seizures, familial, 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at