rs965830

Variant names:

• chr16-24261064-G-T
• rs965830
• NM_006539.4:c.211+4099G>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+4099G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,066 control chromosomes in the GnomAD database, including 21,345 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 0.53 (21345 hom., cov: 32)
• Consequence: CACNG3 NM_006539.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNG3	NM_006539.4	c.211+4099G>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.211+4099G>T		intron_variant	Intron 1 of 3	1	NM_006539.4	ENSP00000005284.4

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80325 AN: 151948 Hom.: 21325 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.529 AC: 80397 AN: 152066 Hom.: 21345 Cov.: 32 AF XY: 0.530 AC XY: 39439 AN XY: 74366

African (AFR) AF: 0.538 AC: 22325 AN: 41468

American (AMR) AF: 0.530 AC: 8094 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1863 AN: 3464

East Asian (EAS) AF: 0.391 AC: 2022 AN: 5174

South Asian (SAS) AF: 0.597 AC: 2880 AN: 4822

European-Finnish (FIN) AF: 0.527 AC: 5572 AN: 10574

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36068 AN: 67966

Other (OTH) AF: 0.528 AC: 1115 AN: 2110

Alfa AF: 0.538 Hom.: 2867

Bravo AF: 0.526

Asia WGS AF: 0.525 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.65
PhyloP100		-0.035
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: rs965830; hg19: chr16-24272385;