16-24279732-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006539.4(CACNG3):​c.211+22767T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,058 control chromosomes in the GnomAD database, including 11,980 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 0.40 ( 11980 hom., cov: 32)

Consequence

CACNG3
NM_006539.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00400
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CACNG3NM_006539.4 linkuse as main transcriptc.211+22767T>A intron_variant ENST00000005284.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CACNG3ENST00000005284.4 linkuse as main transcriptc.211+22767T>A intron_variant 1 NM_006539.4 P1

Frequencies

GnomAD3 genomes
AF:
0.395
AC:
60051
AN:
151940
Hom.:
11975
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.414
Gnomad AMI
AF:
0.365
Gnomad AMR
AF:
0.361
Gnomad ASJ
AF:
0.440
Gnomad EAS
AF:
0.305
Gnomad SAS
AF:
0.559
Gnomad FIN
AF:
0.382
Gnomad MID
AF:
0.500
Gnomad NFE
AF:
0.386
Gnomad OTH
AF:
0.406
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.395
AC:
60088
AN:
152058
Hom.:
11980
Cov.:
32
AF XY:
0.397
AC XY:
29474
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.414
Gnomad4 AMR
AF:
0.361
Gnomad4 ASJ
AF:
0.440
Gnomad4 EAS
AF:
0.305
Gnomad4 SAS
AF:
0.559
Gnomad4 FIN
AF:
0.382
Gnomad4 NFE
AF:
0.386
Gnomad4 OTH
AF:
0.404
Alfa
AF:
0.392
Hom.:
1462
Bravo
AF:
0.388
Asia WGS
AF:
0.427
AC:
1489
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.3
DANN
Benign
0.54

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs991911; hg19: chr16-24291053; API