16-24308373-T-C

Variant names:

• chr16-24308373-T-C
• rs757200
• NM_006539.4:c.212-38361T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006539.4(CACNG3):​c.212-38361T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 152,016 control chromosomes in the GnomAD database, including 45,517 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 0.77 (45517 hom., cov: 30)
• Consequence: CACNG3 NM_006539.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNG3	NM_006539.4	c.212-38361T>C		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.212-38361T>C		intron_variant	Intron 1 of 3	1	NM_006539.4	ENSP00000005284.4

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116241 AN: 151898 Hom.: 45461 Cov.: 30

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.765 AC: 116352 AN: 152016 Hom.: 45517 Cov.: 30 AF XY: 0.763 AC XY: 56643 AN XY: 74284

African (AFR) AF: 0.942 AC: 39074 AN: 41496

American (AMR) AF: 0.674 AC: 10290 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2516 AN: 3472

East Asian (EAS) AF: 0.612 AC: 3144 AN: 5136

South Asian (SAS) AF: 0.800 AC: 3852 AN: 4812

European-Finnish (FIN) AF: 0.677 AC: 7157 AN: 10566

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47820 AN: 67948

Other (OTH) AF: 0.755 AC: 1595 AN: 2112

Alfa AF: 0.718 Hom.: 24026

Bravo AF: 0.768

Asia WGS AF: 0.753 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.61
DANN	Benign	0.58
PhyloP100		-1.2
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: rs757200; hg19: chr16-24319694;