Variant rs12928078 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_006539.4(CACNG3):c.921G>A(p.Pro307Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0403 in 1,610,680 control chromosomes in the GnomAD database, including 1,504 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 0.033 ( 117 hom., cov: 31)

Exomes 𝑓: 0.041 ( 1387 hom. )

Consequence

CACNG3
NM_006539.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.216

Variant links:

Genes affected

CACNG3 (HGNC:1407): (calcium voltage-gated channel auxiliary subunit gamma 3) The protein encoded by this gene is a type I transmembrane AMPA receptor regulatory protein (TARP). TARPs regulate both trafficking and channel gating of the AMPA receptors. This gene is part of a functionally diverse eight-member protein subfamily of the PMP-22/EMP/MP20 family. This gene is a susceptibility locus for childhood absence epilepsy. [provided by RefSeq, Dec 2010]

CACNG3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP7

Synonymous conserved (PhyloP=-0.216 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNG3	NM_006539.4 linkuse as main transcript	c.921G>A	p.Pro307Pro	synonymous_variant	4/4	ENST00000005284.4	NP_006530.1	O60359

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNG3	ENST00000005284.4 linkuse as main transcript	c.921G>A	p.Pro307Pro	synonymous_variant	4/4	1	NM_006539.4	ENSP00000005284.4		O60359

Frequencies

GnomAD3 genomes

AF:

0.0333

AC:

5066

AN:

152032

Hom.:

117

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0158

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0210

Gnomad ASJ

AF:

0.0320

Gnomad EAS

AF:

0.000771

Gnomad SAS

AF:

0.0458

Gnomad FIN

AF:

0.0678

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0432

Gnomad OTH

AF:

0.0345

GnomAD3 exomes

AF:

0.0374

AC:

9275

AN:

247904

Hom.:

234

AF XY:

0.0399

AC XY:

5356

AN XY:

134174

show subpopulations

Gnomad AFR exome

AF:

0.0150

Gnomad AMR exome

AF:

0.0162

Gnomad ASJ exome

AF:

0.0233

Gnomad EAS exome

AF:

0.000164

Gnomad SAS exome

AF:

0.0578

Gnomad FIN exome

AF:

0.0684

Gnomad NFE exome

AF:

0.0436

Gnomad OTH exome

AF:

0.0366

GnomAD4 exome

AF:

0.0410

AC:

59822

AN:

1458530

Hom.:

1387

Cov.:

AF XY:

0.0418

AC XY:

30321

AN XY:

725604

show subpopulations

Gnomad4 AFR exome

AF:

0.0149

Gnomad4 AMR exome

AF:

0.0169

Gnomad4 ASJ exome

AF:

0.0237

Gnomad4 EAS exome

AF:

0.000252

Gnomad4 SAS exome

AF:

0.0579

Gnomad4 FIN exome

AF:

0.0677

Gnomad4 NFE exome

AF:

0.0423

Gnomad4 OTH exome

AF:

0.0363

GnomAD4 genome

AF:

0.0333

AC:

5070

AN:

152150

Hom.:

117

Cov.:

AF XY:

0.0334

AC XY:

2485

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.0158

Gnomad4 AMR

AF:

0.0210

Gnomad4 ASJ

AF:

0.0320

Gnomad4 EAS

AF:

0.000773

Gnomad4 SAS

AF:

0.0461

Gnomad4 FIN

AF:

0.0678

Gnomad4 NFE

AF:

0.0432

Gnomad4 OTH

AF:

0.0346

Alfa

AF:

0.0311

Hom.:

Bravo

AF:

0.0286

Asia WGS

AF:

0.0210

AC:

AN:

3478

EpiCase

AF:

0.0436

EpiControl

AF:

0.0443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

9.2

DANN

Benign

0.67

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over