chr6-29610161-A-G

Variant names:

• chr6-29610161-A-G
• rs29259
• NM_001470.4:c.1708+763T>C

Variant summary

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

The NM_001470.4(GABBR1):​c.1708+763T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 151,546 control chromosomes in the GnomAD database, including 2,421 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 0.17 (2421 hom., cov: 31)
• Consequence: GABBR1 NM_001470.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

GABBR1 (HGNC:4070): (gamma-aminobutyric acid type B receptor subunit 1) This gene encodes a receptor for gamma-aminobutyric acid (GABA), which is the main inhibitory neurotransmitter in the mammalian central nervous system. This receptor functions as a heterodimer with GABA(B) receptor 2. Defects in this gene may underlie brain disorders such as schizophrenia and epilepsy. Alternative splicing generates multiple transcript variants, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jan 2016]

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 (SAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABBR1	NM_001470.4	c.1708+763T>C		intron_variant	Intron 14 of 22	ENST00000377034.9	NP_001461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABBR1	ENST00000377034.9	c.1708+763T>C		intron_variant	Intron 14 of 22	1	NM_001470.4	ENSP00000366233.4

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25526 AN: 151460 Hom.: 2420 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.356

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.169 AC: 25537 AN: 151546 Hom.: 2421 Cov.: 31 AF XY: 0.170 AC XY: 12593 AN XY: 73986

African (AFR) AF: 0.155 AC: 6387 AN: 41272

American (AMR) AF: 0.169 AC: 2580 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3464

East Asian (EAS) AF: 0.257 AC: 1327 AN: 5156

South Asian (SAS) AF: 0.318 AC: 1520 AN: 4786

European-Finnish (FIN) AF: 0.0734 AC: 762 AN: 10384

Middle Eastern (MID) AF: 0.347 AC: 100 AN: 288

European-Non Finnish (NFE) AF: 0.170 AC: 11533 AN: 67946

Other (OTH) AF: 0.209 AC: 438 AN: 2100

Alfa AF: 0.164 Hom.: 930

Bravo AF: 0.175

Asia WGS AF: 0.232 AC: 805 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	1.3
DANN	Benign	0.68
PhyloP100		-1.2
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

Publications

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Other links and lift over

dbSNP: rs29259; hg19: chr6-29577938;