chr16-24362448-C-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006539.4(CACNG3):c.*585C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,592 control chromosomes in the GnomAD database, including 2,830 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 0.19 ( 2818 hom., cov: 32)
Exomes 𝑓: 0.22 ( 12 hom. )
Consequence
CACNG3
NM_006539.4 downstream_gene
NM_006539.4 downstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.768
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]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.191 AC: 29023AN: 151948Hom.: 2816 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
29023
AN:
151948
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.219 AC: 115AN: 526Hom.: 12 Cov.: 0 AF XY: 0.226 AC XY: 70AN XY: 310 show subpopulations
GnomAD4 exome
AF:
AC:
115
AN:
526
Hom.:
Cov.:
0
AF XY:
AC XY:
70
AN XY:
310
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
AC:
2
AN:
4
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
AC:
0
AN:
2
European-Finnish (FIN)
AF:
AC:
99
AN:
426
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
12
AN:
88
Other (OTH)
AF:
AC:
2
AN:
6
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.465
Heterozygous variant carriers
0
6
13
19
26
32
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Hom
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.191 AC: 29042AN: 152066Hom.: 2818 Cov.: 32 AF XY: 0.193 AC XY: 14334AN XY: 74328 show subpopulations
GnomAD4 genome
AF:
AC:
29042
AN:
152066
Hom.:
Cov.:
32
AF XY:
AC XY:
14334
AN XY:
74328
show subpopulations
African (AFR)
AF:
AC:
8057
AN:
41442
American (AMR)
AF:
AC:
2879
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
844
AN:
3470
East Asian (EAS)
AF:
AC:
282
AN:
5176
South Asian (SAS)
AF:
AC:
966
AN:
4814
European-Finnish (FIN)
AF:
AC:
2420
AN:
10562
Middle Eastern (MID)
AF:
AC:
65
AN:
294
European-Non Finnish (NFE)
AF:
AC:
12988
AN:
68002
Other (OTH)
AF:
AC:
396
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1185
2370
3554
4739
5924
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
304
608
912
1216
1520
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
450
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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