rs2189290

Variant names:

• chr16-24345212-C-T
• rs2189290
• NM_006539.4:c.212-1522C>T

Variant summary

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

The NM_006539.4(CACNG3):​c.212-1522C>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
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006539.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNG3	NM_006539.4	MANE Select	c.212-1522C>T		intron	N/A	NP_006530.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNG3	ENST00000005284.4	TSL:1 MANE Select	c.212-1522C>T		intron	N/A	ENSP00000005284.4

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

African (AFR) AF: 0.836 AC: 34693 AN: 41510

American (AMR) AF: 0.753 AC: 11512 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2538 AN: 3468

East Asian (EAS) AF: 0.701 AC: 3626 AN: 5170

South Asian (SAS) AF: 0.602 AC: 2890 AN: 4804

European-Finnish (FIN) AF: 0.709 AC: 7485 AN: 10564

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44704 AN: 67960

Other (OTH) AF: 0.722 AC: 1527 AN: 2114

Alfa AF: 0.684 Hom.: 60441

Bravo AF: 0.733

Asia WGS AF: 0.661 AC: 2299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.84
PhyloP100		-0.18
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: rs2189290; hg19: chr16-24356533;