chr5-161293870-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001371727.1(GABRB2):c.*211C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0263 in 545,512 control chromosomes in the GnomAD database, including 244 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.022 ( 47 hom., cov: 32)
Exomes 𝑓: 0.028 ( 197 hom. )
Consequence
GABRB2
NM_001371727.1 3_prime_UTR
NM_001371727.1 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.430
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
?
Variant 5-161293870-G-A is Benign according to our data. Variant chr5-161293870-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1217644.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0222 (3373/152242) while in subpopulation NFE AF= 0.0357 (2425/68002). AF 95% confidence interval is 0.0345. There are 47 homozygotes in gnomad4. There are 1557 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 3373 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRB2 | NM_001371727.1 | c.*211C>T | 3_prime_UTR_variant | 10/10 | ENST00000393959.6 | ||
GABRB2 | NM_000813.3 | c.*211C>T | 3_prime_UTR_variant | 10/10 | |||
GABRB2 | NM_021911.3 | c.*211C>T | 3_prime_UTR_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRB2 | ENST00000393959.6 | c.*211C>T | 3_prime_UTR_variant | 10/10 | 1 | NM_001371727.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0222 AC: 3373AN: 152124Hom.: 47 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
3373
AN:
152124
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:
GnomAD4 exome AF: 0.0280 AC: 10996AN: 393270Hom.: 197 Cov.: 3 AF XY: 0.0275 AC XY: 5633AN XY: 204642
GnomAD4 exome
AF:
AC:
10996
AN:
393270
Hom.:
Cov.:
3
AF XY:
AC XY:
5633
AN XY:
204642
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: 0.0222 AC: 3373AN: 152242Hom.: 47 Cov.: 32 AF XY: 0.0209 AC XY: 1557AN XY: 74438
GnomAD4 genome
?
AF:
AC:
3373
AN:
152242
Hom.:
Cov.:
32
AF XY:
AC XY:
1557
AN XY:
74438
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:
Asia WGS
AF:
AC:
19
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 06, 2018 | - - |
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