NM_006539.4:c.212-37615A>G

Variant names:

• chr16-24309119-A-G
• rs9921785
• NM_006539.4:c.212-37615A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006539.4(CACNG3):​c.212-37615A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,006 control chromosomes in the GnomAD database, including 8,859 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 0.33 (8859 hom., cov: 31)
• Consequence: CACNG3 NM_006539.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471
• Publications: 4 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNG3	NM_006539.4	c.212-37615A>G		intron_variant	Intron 1 of 3	ENST00000005284.4	NP_006530.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNG3	ENST00000005284.4	c.212-37615A>G		intron_variant	Intron 1 of 3	1	NM_006539.4	ENSP00000005284.4

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50021 AN: 151888 Hom.: 8861 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.329 AC: 50021 AN: 152006 Hom.: 8859 Cov.: 31 AF XY: 0.326 AC XY: 24239 AN XY: 74268

African (AFR) AF: 0.220 AC: 9128 AN: 41516

American (AMR) AF: 0.290 AC: 4426 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1339 AN: 3464

East Asian (EAS) AF: 0.384 AC: 1980 AN: 5154

South Asian (SAS) AF: 0.560 AC: 2700 AN: 4818

European-Finnish (FIN) AF: 0.245 AC: 2584 AN: 10542

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26530 AN: 67930

Other (OTH) AF: 0.350 AC: 739 AN: 2110

Alfa AF: 0.369 Hom.: 24499

Bravo AF: 0.322

Asia WGS AF: 0.467 AC: 1620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.43
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9921785; hg19: chr16-24320440;