Genetic Variant CACNG3:c.*585C>G (chr16-24362448-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006539.4(CACNG3):c.*585C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,592 control chromosomes in the GnomAD database, including 2,830 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 0.19 ( 2818 hom., cov: 32)

Exomes 𝑓: 0.22 ( 12 hom. )

Consequence

CACNG3
NM_006539.4 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.768

Publications

3 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNG3	NM_006539.4 link	c.*585C>G		downstream_gene_variant		ENST00000005284.4	NP_006530.1	O60359

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNG3	ENST00000005284.4 link	c.*585C>G		downstream_gene_variant		1	NM_006539.4	ENSP00000005284.4		O60359

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

29023

AN:

151948

Hom.:

2816

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.159

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.243

Gnomad EAS

AF:

0.0542

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.229

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.190

GnomAD4 exome

AF:

0.219

AC:

115

AN:

526

Hom.:

Cov.:

AF XY:

0.226

AC XY:

AN XY:

310

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.232

AC:

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.136

AC:

AN:

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.191

AC:

29042

AN:

152066

Hom.:

2818

Cov.:

AF XY:

0.193

AC XY:

14334

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.194

AC:

8057

AN:

41442

American (AMR)

AF:

0.188

AC:

2879

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.243

AC:

844

AN:

3470

East Asian (EAS)

AF:

0.0545

AC:

282

AN:

5176

South Asian (SAS)

AF:

0.201

AC:

966

AN:

4814

European-Finnish (FIN)

AF:

0.229

AC:

2420

AN:

10562

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.191

AC:

12988

AN:

68002

Other (OTH)

AF:

0.188

AC:

396

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1185

2370

3554

4739

5924

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

304

608

912

1216

1520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.192

Hom.:

374

Bravo

AF:

0.186

Asia WGS

AF:

0.129

AC:

450

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

(source)

DANN

Benign

0.65

PhyloP100

0.77

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over