chr15-26989406-G-A

Variant names:

• chr15-26989406-G-A
• rs11635092
• NM_033223.5:c.202+12256G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033223.5(GABRG3):​c.202+12256G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,034 control chromosomes in the GnomAD database, including 6,767 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6767 hom., cov: 33)
• Consequence: GABRG3 NM_033223.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.701
• Publications: 1 publications found

Genes affected

GABRG3 (HGNC:4088): (gamma-aminobutyric acid type A receptor subunit gamma3) This gene encodes a gamma-aminobutyric acid (GABA) receptor. GABA is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA-A receptors, which are ligand-gated chloride channels. Chloride conductance of these channels can be modulated by agents such as benzodiazepines that bind to the GABA-A receptor. GABA-A receptors are pentameric, consisting of proteins from several subunit classes: alpha, beta, gamma, delta and rho. The protein encoded by this gene is a gamma subunit, which contains the benzodiazepine binding site. Two transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Aug 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABRG3	NM_033223.5	c.202+12256G>A		intron_variant	Intron 2 of 9	ENST00000615808.5	NP_150092.2
GABRG3	NM_001270873.2	c.202+12256G>A		intron_variant	Intron 2 of 5		NP_001257802.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRG3	ENST00000615808.5	c.202+12256G>A		intron_variant	Intron 2 of 9	1	NM_033223.5	ENSP00000479113.1
GABRG3	ENST00000555083.5	c.202+12256G>A		intron_variant	Intron 2 of 5	2		ENSP00000452244.1
GABRG3	ENST00000553440.1	n.294+12256G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43201 AN: 151916 Hom.: 6762 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.309

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.284 AC: 43222 AN: 152034 Hom.: 6767 Cov.: 33 AF XY: 0.275 AC XY: 20461 AN XY: 74334

African (AFR) AF: 0.189 AC: 7836 AN: 41480

American (AMR) AF: 0.274 AC: 4193 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1278 AN: 3466

East Asian (EAS) AF: 0.181 AC: 938 AN: 5176

South Asian (SAS) AF: 0.173 AC: 832 AN: 4818

European-Finnish (FIN) AF: 0.233 AC: 2469 AN: 10584

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24648 AN: 67912

Other (OTH) AF: 0.309 AC: 651 AN: 2106

Alfa AF: 0.320 Hom.: 1098

Bravo AF: 0.286

Asia WGS AF: 0.168 AC: 588 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.41
PhyloP100		0.70
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11635092; hg19: chr15-27234553;