15-27025278-T-A

Variant names:

• chr15-27025278-T-A
• rs6606858
• NM_033223.5:c.203-1476T>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.203-1476T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 151,998 control chromosomes in the GnomAD database, including 33,550 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 0.66 (33550 hom., cov: 32)
• Consequence: GABRG3 NM_033223.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.962
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABRG3	NM_033223.5	c.203-1476T>A		intron_variant	Intron 2 of 9	ENST00000615808.5	NP_150092.2
GABRG3	NM_001270873.2	c.203-1476T>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.203-1476T>A		intron_variant	Intron 2 of 9	1	NM_033223.5	ENSP00000479113.1
GABRG3	ENST00000555083.5	c.203-1476T>A		intron_variant	Intron 2 of 5	2		ENSP00000452244.1
GABRG3	ENST00000553440.1	n.295-1476T>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100739 AN: 151880 Hom.: 33526 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.663 AC: 100818 AN: 151998 Hom.: 33550 Cov.: 32 AF XY: 0.664 AC XY: 49362 AN XY: 74292

African (AFR) AF: 0.712 AC: 29485 AN: 41438

American (AMR) AF: 0.654 AC: 9994 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2446 AN: 3470

East Asian (EAS) AF: 0.689 AC: 3539 AN: 5138

South Asian (SAS) AF: 0.660 AC: 3180 AN: 4820

European-Finnish (FIN) AF: 0.657 AC: 6944 AN: 10568

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 42993 AN: 67966

Other (OTH) AF: 0.655 AC: 1384 AN: 2112

Alfa AF: 0.646 Hom.: 3939

Bravo AF: 0.666

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.54
PhyloP100		0.96
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: rs6606858; hg19: chr15-27270425;