3-98019352-T-C

Variant names:

• chr3-98019352-T-C
• rs854579
• NM_001105580.3:c.239-1630A>G

Variant summary

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

The NM_001105580.3(GABRR3):​c.239-1630A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,016 control chromosomes in the GnomAD database, including 6,220 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 0.26 (6220 hom., cov: 31)
• Consequence: GABRR3 NM_001105580.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 6 publications found

Genes affected

GABRR3 (HGNC:17969): (gamma-aminobutyric acid type A receptor subunit rho3) The neurotransmitter gamma-aminobutyric acid (GABA) functions in the central nervous system to regulate synaptic transmission of neurons. This gene encodes one of three related subunits, which combine as homo- or hetero-pentamers to form GABA(C) receptors. In humans, some individuals contain a single-base polymorphism (dbSNP rs832032) that is predicted to inactivate the gene product. [provided by RefSeq, Jan 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001105580.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRR3	NM_001105580.3	MANE Select	c.239-1630A>G		intron	N/A	NP_001099050.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GABRR3	ENST00000472788.6	TSL:5 MANE Select	c.239-1630A>G		intron	N/A	ENSP00000420790.1
	GABRR3	ENST00000470589.1	TSL:1	n.356-1630A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39715 AN: 151898 Hom.: 6223 Cov.: 31

Gnomad AFR AF: 0.0768

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.261 AC: 39707 AN: 152016 Hom.: 6220 Cov.: 31 AF XY: 0.266 AC XY: 19745 AN XY: 74298

African (AFR) AF: 0.0767 AC: 3185 AN: 41540

American (AMR) AF: 0.301 AC: 4597 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3468

East Asian (EAS) AF: 0.433 AC: 2215 AN: 5118

South Asian (SAS) AF: 0.359 AC: 1727 AN: 4804

European-Finnish (FIN) AF: 0.372 AC: 3925 AN: 10542

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22248 AN: 67954

Other (OTH) AF: 0.272 AC: 574 AN: 2110

Alfa AF: 0.311 Hom.: 5216

Bravo AF: 0.244

Asia WGS AF: 0.363 AC: 1263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.59
PhyloP100		-0.10

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: rs854579; hg19: chr3-97738196;