rs8052039

Positions:

• chr16-24296075-A-G
• chr16-24296075-A-T

Variant summary

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

The NM_006539.4(CACNG3):​c.211+39110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,148 control chromosomes in the GnomAD database, including 50,262 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 0.81 (50262 hom., cov: 31)
• Consequence: CACNG3 NM_006539.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNG3	NM_006539.4	c.211+39110A>G		intron_variant		ENST00000005284.4	NP_006530.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNG3	ENST00000005284.4	c.211+39110A>G		intron_variant		1	NM_006539.4	ENSP00000005284	P1

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122921 AN: 152030 Hom.: 50206 Cov.: 31

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.809 AC: 123038 AN: 152148 Hom.: 50262 Cov.: 31 AF XY: 0.806 AC XY: 59986 AN XY: 74380

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.799

Alfa AF: 0.773 Hom.: 66444

Bravo AF: 0.810

Asia WGS AF: 0.845 AC: 2941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0020
DANN	Benign	0.45

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: rs8052039; hg19: chr16-24307396;