rs1557809

chr16-24297787-T-C

Variant summary

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

The NM_006539.4(CACNG3):c.211+40822T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,122 control chromosomes in the GnomAD database, including 2,530 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 0.17 (2530 hom., cov: 32)
• Consequence: CACNG3 NM_006539.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNG3	NM_006539.4	c.211+40822T>C		intron_variant		ENST00000005284.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNG3	ENST00000005284.4	c.211+40822T>C		intron_variant		1	NM_006539.4	P1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26229 AN: 152004 Hom.: 2529 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.172 AC: 26232 AN: 152122 Hom.: 2530 Cov.: 32 AF XY: 0.176 AC XY: 13085 AN XY: 74374

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.192

Alfa AF: 0.183 Hom.: 3573

Bravo AF: 0.161

Asia WGS AF: 0.337 AC: 1172 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.41
Dann	Benign	0.66

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: rs1557809; hg19: chr16-24309108;