NM_002042.5:c.797-1386C>T

Variant names:

• chr6-89183443-G-A
• rs368873
• NM_002042.5:c.797-1386C>T

Variant summary

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

The NM_002042.5(GABRR1):​c.797-1386C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 151,980 control chromosomes in the GnomAD database, including 33,646 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 (33646 hom., cov: 31)
• Consequence: GABRR1 NM_002042.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 5 publications found

Genes affected

GABRR1 (HGNC:4090): (gamma-aminobutyric acid type A receptor subunit rho1) GABA is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA receptors, which are ligand-gated chloride channels. GABRR1 is a member of the rho subunit family. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABRR1	NM_002042.5	c.797-1386C>T		intron_variant	Intron 7 of 9	ENST00000454853.7	NP_002033.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRR1	ENST00000454853.7	c.797-1386C>T		intron_variant	Intron 7 of 9	1	NM_002042.5	ENSP00000412673.2
GABRR1	ENST00000435811.5	c.746-1386C>T		intron_variant	Intron 6 of 8	2		ENSP00000394687.1
GABRR1	ENST00000369451.7	c.536-1386C>T		intron_variant	Intron 9 of 11	5		ENSP00000358463.3
GABRR1	ENST00000457434.1	n.*758-1386C>T		intron_variant	Intron 8 of 10	5		ENSP00000410130.1

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100435 AN: 151862 Hom.: 33606 Cov.: 31

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.662 AC: 100541 AN: 151980 Hom.: 33646 Cov.: 31 AF XY: 0.652 AC XY: 48415 AN XY: 74270

African (AFR) AF: 0.616 AC: 25517 AN: 41422

American (AMR) AF: 0.646 AC: 9857 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2581 AN: 3472

East Asian (EAS) AF: 0.367 AC: 1897 AN: 5162

South Asian (SAS) AF: 0.637 AC: 3066 AN: 4814

European-Finnish (FIN) AF: 0.624 AC: 6574 AN: 10538

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48775 AN: 67984

Other (OTH) AF: 0.697 AC: 1474 AN: 2114

Alfa AF: 0.704 Hom.: 23802

Bravo AF: 0.661

Asia WGS AF: 0.560 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.4
DANN	Benign	0.34
PhyloP100		0.26
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: rs368873; hg19: chr6-89893162;