16-24281517-G-A

Variant names:

• chr16-24281517-G-A
• rs2247011
• NM_006539.4:c.211+24552G>A

Variant summary

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

The NM_006539.4(CACNG3):​c.211+24552G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 151,976 control chromosomes in the GnomAD database, including 37,728 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 0.70 (37728 hom., cov: 31)
• Consequence: CACNG3 NM_006539.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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.211+24552G>A		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.211+24552G>A		intron	N/A	ENSP00000005284.4

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106784 AN: 151858 Hom.: 37700 Cov.: 31

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.703 AC: 106864 AN: 151976 Hom.: 37728 Cov.: 31 AF XY: 0.703 AC XY: 52233 AN XY: 74282

African (AFR) AF: 0.713 AC: 29524 AN: 41422

American (AMR) AF: 0.651 AC: 9942 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2419 AN: 3470

East Asian (EAS) AF: 0.827 AC: 4274 AN: 5170

South Asian (SAS) AF: 0.786 AC: 3778 AN: 4808

European-Finnish (FIN) AF: 0.701 AC: 7396 AN: 10552

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47300 AN: 67972

Other (OTH) AF: 0.694 AC: 1468 AN: 2114

Alfa AF: 0.695 Hom.: 122140

Bravo AF: 0.697

Asia WGS AF: 0.781 AC: 2717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0080
DANN	Benign	0.12
PhyloP100		-1.6
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: rs2247011; hg19: chr16-24292838;