chr15-26672011-C-T

Position:

• chr15-26672011-C-T

Variant summary

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

The NM_000814.6(GABRB3):​c.241-50477G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,948 control chromosomes in the GnomAD database, including 5,291 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 0.24 (5291 hom., cov: 32)
• Consequence: GABRB3 NM_000814.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRB3	NM_000814.6	c.241-50477G>A		intron_variant		ENST00000311550.10
GABRB3	NM_001191320.2	c.-16+44603G>A		intron_variant
GABRB3	NM_001278631.2	c.-111-29483G>A		intron_variant
GABRB3	NM_021912.5	c.241-50477G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRB3	ENST00000311550.10	c.241-50477G>A		intron_variant		1	NM_000814.6	P1

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36160 AN: 151830 Hom.: 5286 Cov.: 32

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.238 AC: 36171 AN: 151948 Hom.: 5291 Cov.: 32 AF XY: 0.241 AC XY: 17904 AN XY: 74256

Gnomad4 AFR AF: 0.0612

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.239

Alfa AF: 0.287 Hom.: 3418

Bravo AF: 0.231

Asia WGS AF: 0.324 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.38

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: rs1367959; hg19: chr15-26917158;