rs2189290

Positions:

• chr16-24345212-C-T

Variant summary

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

The NM_006539.4(CACNG3):​c.212-1522C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,080 control chromosomes in the GnomAD database, including 40,215 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 0.72 (40215 hom., cov: 32)
• Consequence: CACNG3 NM_006539.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNG3	NM_006539.4	c.212-1522C>T		intron_variant		ENST00000005284.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNG3	ENST00000005284.4	c.212-1522C>T		intron_variant		1	NM_006539.4	P1

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109717 AN: 151962 Hom.: 40165 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.722 AC: 109827 AN: 152080 Hom.: 40215 Cov.: 32 AF XY: 0.722 AC XY: 53677 AN XY: 74336

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.722

Alfa AF: 0.678 Hom.: 46896

Bravo AF: 0.733

Asia WGS AF: 0.661 AC: 2299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.84

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: rs2189290; hg19: chr16-24356533;