chr15-26707147-T-C

Position:

• chr15-26707147-T-C

Variant summary

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

The NM_000814.6(GABRB3):​c.240+65255A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,130 control chromosomes in the GnomAD database, including 41,380 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 0.72 (41380 hom., cov: 33)
• Consequence: GABRB3 NM_000814.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159

Genes affected

GABRB3 (HGNC:4083): (gamma-aminobutyric acid type A receptor subunit beta3) This gene encodes a member of the ligand-gated ionic channel family. The encoded protein is one the subunits of a multi-subunit chloride channel that serves as the receptor for gamma-aminobutyric acid, a major inhibitory neurotransmitter of the mammalian nervous system. This gene is located on the long arm of chromosome 15 in a cluster with two other genes encoding related subunits of the family. This gene may be associated with the pathogenesis of several disorders including Angelman syndrome, Prader-Willi syndrome, nonsyndromic orofacial clefts, epilepsy and autism. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2013]

ACMG classification

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 = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRB3	NM_000814.6	c.240+65255A>G		intron_variant		ENST00000311550.10
GABRB3	NM_001191320.2	c.-16+9467A>G		intron_variant
GABRB3	NM_001278631.2	c.-111-64619A>G		intron_variant
GABRB3	NM_021912.5	c.240+65255A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRB3	ENST00000311550.10	c.240+65255A>G		intron_variant		1	NM_000814.6	P1

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109594 AN: 152012 Hom.: 41360 Cov.: 33

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.721 AC: 109660 AN: 152130 Hom.: 41380 Cov.: 33 AF XY: 0.728 AC XY: 54189 AN XY: 74388

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.853

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.758

Alfa AF: 0.781 Hom.: 24322

Bravo AF: 0.701

Asia WGS AF: 0.811 AC: 2819 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	4.3
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1426223; hg19: chr15-26952294;