rs3219151

Variant names:

• chr5-161701908-C-A
• rs3219151
• NM_000811.3:c.*135C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-161701908-C-A
• chr5-161701908-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000811.3(GABRA6):​c.*135C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GABRA6 NM_000811.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520
• Publications: 49 publications found

Genes affected

GABRA6 (HGNC:4080): (gamma-aminobutyric acid type A receptor subunit alpha6) GABA is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA-A receptors, which are ligand-gated chloride channels. Chloride conductance of these channels can be modulated by agents such as benzodiazepines that bind to the GABA-A receptor. At least 16 distinct subunits of GABA-A receptors have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABRA6	NM_000811.3	c.*135C>A		3_prime_UTR_variant	Exon 9 of 9	ENST00000274545.10	NP_000802.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRA6	ENST00000274545.10	c.*135C>A		3_prime_UTR_variant	Exon 9 of 9	1	NM_000811.3	ENSP00000274545.5
GABRA6	ENST00000521520.1	n.1490C>A		non_coding_transcript_exon_variant	Exon 3 of 3	2
GABRA6	ENST00000523217.5	c.*135C>A		3_prime_UTR_variant	Exon 9 of 9	5		ENSP00000430527.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 787866 Hom.: 0 Cov.: 10 AF XY: 0.00 AC XY: 0 AN XY: 408596

African (AFR) AF: 0.00 AC: 0 AN: 19456

American (AMR) AF: 0.00 AC: 0 AN: 34594

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19996

East Asian (EAS) AF: 0.00 AC: 0 AN: 34146

South Asian (SAS) AF: 0.00 AC: 0 AN: 63980

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37074

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3170

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 537534

Other (OTH) AF: 0.00 AC: 0 AN: 37916

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 86587

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.51
PhyloP100		0.52

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: rs3219151; hg19: chr5-161128914;