chr5-161294090-A-G
Position:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001371727.1(GABRB2):āc.1530T>Cā(p.Tyr510=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,610,300 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.000053 ( 1 hom., cov: 32)
Exomes š: 0.000021 ( 0 hom. )
Consequence
GABRB2
NM_001371727.1 synonymous
NM_001371727.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.82
Genes affected
GABRB2 (HGNC:4082): (gamma-aminobutyric acid type A receptor subunit beta2) The gamma-aminobutyric acid (GABA) A receptor is a multisubunit chloride channel that mediates the fastest inhibitory synaptic transmission in the central nervous system. This gene encodes GABA A receptor, beta 2 subunit. It is mapped to chromosome 5q34 in a cluster comprised of genes encoding alpha 1 and gamma 2 subunits of the GABA A receptor. Alternative splicing of this gene generates 2 transcript variants, differing by a 114 bp insertion. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 5-161294090-A-G is Benign according to our data. Variant chr5-161294090-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 533532.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.82 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0000525 (8/152326) while in subpopulation AMR AF= 0.000327 (5/15306). AF 95% confidence interval is 0.000129. There are 1 homozygotes in gnomad4. There are 3 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRB2 | NM_001371727.1 | c.1530T>C | p.Tyr510= | synonymous_variant | 10/10 | ENST00000393959.6 | |
GABRB2 | NM_021911.3 | c.1530T>C | p.Tyr510= | synonymous_variant | 11/11 | ||
GABRB2 | NM_000813.3 | c.1416T>C | p.Tyr472= | synonymous_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRB2 | ENST00000393959.6 | c.1530T>C | p.Tyr510= | synonymous_variant | 10/10 | 1 | NM_001371727.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152208Hom.: 1 Cov.: 32
GnomAD3 genomes
AF:
AC:
8
AN:
152208
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000758 AC: 19AN: 250752Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135548
GnomAD3 exomes
AF:
AC:
19
AN:
250752
Hom.:
AF XY:
AC XY:
9
AN XY:
135548
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1457974Hom.: 0 Cov.: 30 AF XY: 0.0000207 AC XY: 15AN XY: 724654
GnomAD4 exome
AF:
AC:
30
AN:
1457974
Hom.:
Cov.:
30
AF XY:
AC XY:
15
AN XY:
724654
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152326Hom.: 1 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74480
GnomAD4 genome
AF:
AC:
8
AN:
152326
Hom.:
Cov.:
32
AF XY:
AC XY:
3
AN XY:
74480
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2021 | - - |
Intellectual disability Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at