rs72831507

chr6-29617966-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001470.4(GABBR1):c.1323+3135C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.055 in 152,212 control chromosomes in the GnomAD database, including 336 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 0.055 (336 hom., cov: 32)
• Consequence: GABBR1 NM_001470.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABBR1	NM_001470.4	c.1323+3135C>A		intron_variant		ENST00000377034.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABBR1	ENST00000377034.9	c.1323+3135C>A		intron_variant		1	NM_001470.4	P1

Frequencies

GnomAD3 genomes AF: 0.0550 AC: 8360 AN: 152094 Hom.: 334 Cov.: 32

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0340

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0557

Gnomad OTH AF: 0.0646

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

GnomAD4 genome AF: 0.0550 AC: 8366 AN: 152212 Hom.: 336 Cov.: 32 AF XY: 0.0573 AC XY: 4263 AN XY: 74412

Gnomad4 AFR AF: 0.0426

Gnomad4 AMR AF: 0.0507

Gnomad4 ASJ AF: 0.0357

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0340

Gnomad4 NFE AF: 0.0557

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0537 Hom.: 24

Bravo AF: 0.0543

Asia WGS AF: 0.0920 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	10
Dann	Benign	0.77

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

LitVar

Other links and lift over

dbSNP: rs72831507; hg19: chr6-29585743;