15-26757739-A-T

Variant names:

• chr15-26757739-A-T
• rs7178713
• NM_000814.6:c.240+14663T>A

Variant summary

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

The NM_000814.6(GABRB3):​c.240+14663T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,120 control chromosomes in the GnomAD database, including 9,162 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 0.34 (9162 hom., cov: 32)
• Consequence: GABRB3 NM_000814.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

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]

LOC112268151 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GABRB3	NM_000814.6	c.240+14663T>A		intron_variant	Intron 3 of 8	ENST00000311550.10	NP_000805.1
GABRB3	NM_021912.5	c.240+14663T>A		intron_variant	Intron 3 of 8		NP_068712.1
GABRB3	NM_001278631.2	c.-112+14663T>A		intron_variant	Intron 3 of 9		NP_001265560.1
LOC112268151	XR_002957720.2	n.4800-7589T>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GABRB3	ENST00000311550.10	c.240+14663T>A		intron_variant	Intron 3 of 8	1	NM_000814.6	ENSP00000308725.5

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51156 AN: 152002 Hom.: 9136 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.337 AC: 51224 AN: 152120 Hom.: 9162 Cov.: 32 AF XY: 0.334 AC XY: 24872 AN XY: 74360

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.316

Alfa AF: 0.204 Hom.: 410

Bravo AF: 0.329

Asia WGS AF: 0.191 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.83

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: rs7178713; hg19: chr15-27002886;