chr16-24328817-C-T

Variant names:

• chr16-24328817-C-T
• rs2238518
• NM_006539.4:c.212-17917C>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.212-17917C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,794 control chromosomes in the GnomAD database, including 22,786 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 0.54 (22786 hom., cov: 30)
• Consequence: CACNG3 NM_006539.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNG3	NM_006539.4	c.212-17917C>T		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.212-17917C>T		intron_variant	Intron 1 of 3	1	NM_006539.4	ENSP00000005284.4

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81936 AN: 151676 Hom.: 22779 Cov.: 30

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.540 AC: 81978 AN: 151794 Hom.: 22786 Cov.: 30 AF XY: 0.543 AC XY: 40277 AN XY: 74154

African (AFR) AF: 0.439 AC: 18151 AN: 41366

American (AMR) AF: 0.595 AC: 9077 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2607 AN: 3466

East Asian (EAS) AF: 0.655 AC: 3363 AN: 5136

South Asian (SAS) AF: 0.695 AC: 3338 AN: 4800

European-Finnish (FIN) AF: 0.511 AC: 5386 AN: 10534

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.561 AC: 38069 AN: 67916

Other (OTH) AF: 0.577 AC: 1216 AN: 2108

Alfa AF: 0.559 Hom.: 88044

Bravo AF: 0.538

Asia WGS AF: 0.636 AC: 2215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.46
PhyloP100		-0.94
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: rs2238518; hg19: chr16-24340138;