chr6-29610161-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
GABBR1NM_001470.4 linkuse as main transcriptc.1708+763T>C intron_variant ENST00000377034.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GABBR1ENST00000377034.9 linkuse as main transcriptc.1708+763T>C intron_variant 1 NM_001470.4 P1Q9UBS5-1

Frequencies

GnomAD3 genomes
AF:
0.169
AC:
25526
AN:
151460
Hom.:
2420
Cov.:
31
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.155
Gnomad4 AMR
AF:
0.169
Gnomad4 ASJ
AF:
0.216
Gnomad4 EAS
AF:
0.257
Gnomad4 SAS
AF:
0.318
Gnomad4 FIN
AF:
0.0734
Gnomad4 NFE
AF:
0.170
Gnomad4 OTH
AF:
0.209
Alfa
AF:
0.159
Hom.:
529
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

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs29259; hg19: chr6-29577938; API