NM_006539.4:c.211+11817G>T

Variant names:

• chr16-24268782-G-T
• rs8048987
• NM_006539.4:c.211+11817G>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.211+11817G>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 152,046 control chromosomes in the GnomAD database, including 40,069 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 (40069 hom., cov: 32)
• Consequence: CACNG3 NM_006539.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNG3	NM_006539.4	MANE Select	c.211+11817G>T		intron	N/A	NP_006530.1	O60359

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNG3	ENST00000005284.4	TSL:1 MANE Select	c.211+11817G>T		intron	N/A	ENSP00000005284.4	O60359
	CACNG3	ENST00000876789.1		c.211+11817G>T		intron	N/A	ENSP00000546848.1

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109761 AN: 151928 Hom.: 40032 Cov.: 32

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.722 AC: 109848 AN: 152046 Hom.: 40069 Cov.: 32 AF XY: 0.721 AC XY: 53588 AN XY: 74312

African (AFR) AF: 0.815 AC: 33802 AN: 41462

American (AMR) AF: 0.659 AC: 10065 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2560 AN: 3470

East Asian (EAS) AF: 0.789 AC: 4076 AN: 5166

South Asian (SAS) AF: 0.665 AC: 3205 AN: 4816

European-Finnish (FIN) AF: 0.688 AC: 7260 AN: 10556

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46673 AN: 67986

Other (OTH) AF: 0.721 AC: 1522 AN: 2112

Alfa AF: 0.699 Hom.: 16189

Bravo AF: 0.727

Asia WGS AF: 0.728 AC: 2533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.40
DANN	Benign	0.29
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: rs8048987; hg19: chr16-24280103;