rs8052039

Variant names:

• chr16-24296075-A-G
• rs8052039
• NM_006539.4:c.211+39110A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-24296075-A-G
• chr16-24296075-A-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+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
• 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=-0.96).
• 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 rank	MANE	Protein	UniProt
CACNG3	NM_006539.4	c.211+39110A>G		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.211+39110A>G		intron_variant	Intron 1 of 3	1	NM_006539.4	ENSP00000005284.4

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

African (AFR) AF: 0.926 AC: 38460 AN: 41532

American (AMR) AF: 0.724 AC: 11077 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2776 AN: 3472

East Asian (EAS) AF: 0.833 AC: 4297 AN: 5156

South Asian (SAS) AF: 0.845 AC: 4073 AN: 4820

European-Finnish (FIN) AF: 0.750 AC: 7934 AN: 10580

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51926 AN: 67972

Other (OTH) AF: 0.799 AC: 1689 AN: 2114

Alfa AF: 0.782 Hom.: 120239

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
PhyloP100		-2.2
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: rs8052039; hg19: chr16-24307396;