rs369924266
Variant names:
Variant summary
Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_021098.3(CACNA1H):c.3060G>A(p.Ala1020Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000565 in 1,612,848 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00036 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00059 ( 13 hom. )
Consequence
CACNA1H
NM_021098.3 synonymous
NM_021098.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.45
Publications
0 publications found
Genes affected
CACNA1H (HGNC:1395): (calcium voltage-gated channel subunit alpha1 H) This gene encodes a T-type member of the alpha-1 subunit family, a protein in the voltage-dependent calcium channel complex. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization and consist of a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. The alpha-1 subunit has 24 transmembrane segments and forms the pore through which ions pass into the cell. There are multiple isoforms of each of the proteins in the complex, either encoded by different genes or the result of alternative splicing of transcripts. Alternate transcriptional splice variants, encoding different isoforms, have been characterized for the gene described here. Studies suggest certain mutations in this gene lead to childhood absence epilepsy (CAE). [provided by RefSeq, Jul 2008]
CACNA1H Gene-Disease associations (from GenCC):
- hyperaldosteronism, familial, type IVInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- childhood absence epilepsyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- epilepsy, childhood absence, susceptibility to, 6Inheritance: AD Classification: LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 16-1207427-G-A is Benign according to our data. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-1207427-G-A is described in CliVar as Benign. Clinvar id is 529659.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.45 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.000361 (55/152256) while in subpopulation SAS AF = 0.00995 (48/4824). AF 95% confidence interval is 0.00771. There are 0 homozygotes in GnomAd4. There are 42 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
BS2
High AC in GnomAd4 at 55 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.3060G>A | p.Ala1020Ala | synonymous_variant | Exon 14 of 35 | 1 | NM_021098.3 | ENSP00000334198.7 | ||
CACNA1H | ENST00000569107.6 | c.3060G>A | p.Ala1020Ala | synonymous_variant | Exon 14 of 34 | 1 | ENSP00000454990.2 | |||
CACNA1H | ENST00000711493.1 | c.3060G>A | p.Ala1020Ala | synonymous_variant | Exon 14 of 34 | ENSP00000518778.1 | ||||
CACNA1H | ENST00000565831.7 | c.3060G>A | p.Ala1020Ala | synonymous_variant | Exon 14 of 34 | 1 | ENSP00000455840.1 | |||
CACNA1H | ENST00000711450.1 | c.3060G>A | p.Ala1020Ala | synonymous_variant | Exon 14 of 35 | ENSP00000518762.1 | ||||
CACNA1H | ENST00000564231.6 | c.3060G>A | p.Ala1020Ala | synonymous_variant | Exon 14 of 35 | 1 | ENSP00000457555.2 | |||
CACNA1H | ENST00000638323.1 | c.3021G>A | p.Ala1007Ala | synonymous_variant | Exon 14 of 35 | 5 | ENSP00000492267.1 | |||
CACNA1H | ENST00000562079.6 | c.3060G>A | p.Ala1020Ala | synonymous_variant | Exon 14 of 34 | 1 | ENSP00000454581.2 | |||
CACNA1H | ENST00000711438.1 | c.3021G>A | p.Ala1007Ala | synonymous_variant | Exon 14 of 34 | ENSP00000518754.1 | ||||
CACNA1H | ENST00000711482.1 | c.3060G>A | p.Ala1020Ala | synonymous_variant | Exon 14 of 36 | ENSP00000518771.1 | ||||
CACNA1H | ENST00000711485.1 | c.3060G>A | p.Ala1020Ala | synonymous_variant | Exon 14 of 35 | ENSP00000518774.1 | ||||
CACNA1H | ENST00000711455.1 | c.3060G>A | p.Ala1020Ala | synonymous_variant | Exon 14 of 36 | ENSP00000518768.1 | ||||
CACNA1H | ENST00000711483.1 | c.3060G>A | p.Ala1020Ala | synonymous_variant | Exon 14 of 35 | ENSP00000518772.1 | ||||
CACNA1H | ENST00000711456.1 | c.3060G>A | p.Ala1020Ala | synonymous_variant | Exon 14 of 34 | ENSP00000518769.1 | ||||
CACNA1H | ENST00000621827.2 | n.3060G>A | non_coding_transcript_exon_variant | Exon 14 of 37 | 6 | ENSP00000518766.1 | ||||
CACNA1H | ENST00000637236.3 | n.3060G>A | non_coding_transcript_exon_variant | Exon 14 of 34 | 5 | ENSP00000492650.2 | ||||
CACNA1H | ENST00000639478.1 | n.3060G>A | non_coding_transcript_exon_variant | Exon 14 of 35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*973G>A | non_coding_transcript_exon_variant | Exon 14 of 35 | 5 | ENSP00000491488.1 | ||||
CACNA1H | ENST00000711442.1 | n.*2507G>A | non_coding_transcript_exon_variant | Exon 13 of 34 | ENSP00000518758.1 | |||||
CACNA1H | ENST00000711448.1 | n.3060G>A | non_coding_transcript_exon_variant | Exon 14 of 36 | ENSP00000518760.1 | |||||
CACNA1H | ENST00000711449.1 | n.3060G>A | non_coding_transcript_exon_variant | Exon 14 of 35 | ENSP00000518761.1 | |||||
CACNA1H | ENST00000711451.1 | n.3060G>A | non_coding_transcript_exon_variant | Exon 14 of 36 | ENSP00000518763.1 | |||||
CACNA1H | ENST00000711452.1 | n.3060G>A | non_coding_transcript_exon_variant | Exon 14 of 36 | ENSP00000518764.1 | |||||
CACNA1H | ENST00000711453.1 | n.3060G>A | non_coding_transcript_exon_variant | Exon 14 of 36 | ENSP00000518765.1 | |||||
CACNA1H | ENST00000711484.1 | n.3060G>A | non_coding_transcript_exon_variant | Exon 14 of 35 | ENSP00000518773.1 | |||||
CACNA1H | ENST00000711486.1 | n.3060G>A | non_coding_transcript_exon_variant | Exon 14 of 37 | ENSP00000518775.1 | |||||
CACNA1H | ENST00000711487.1 | n.3060G>A | non_coding_transcript_exon_variant | Exon 14 of 36 | ENSP00000518776.1 | |||||
CACNA1H | ENST00000711488.1 | n.3060G>A | non_coding_transcript_exon_variant | Exon 14 of 35 | ENSP00000518777.1 | |||||
CACNA1H | ENST00000640028.1 | n.*973G>A | 3_prime_UTR_variant | Exon 14 of 35 | 5 | ENSP00000491488.1 | ||||
CACNA1H | ENST00000711442.1 | n.*2507G>A | 3_prime_UTR_variant | Exon 13 of 34 | ENSP00000518758.1 |
Frequencies
GnomAD3 genomes AF: 0.000362 AC: 55AN: 152138Hom.: 0 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
55
AN:
152138
Hom.:
Cov.:
30
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:
GnomAD2 exomes AF: 0.00106 AC: 263AN: 246968 AF XY: 0.00136 show subpopulations
GnomAD2 exomes
AF:
AC:
263
AN:
246968
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000587 AC: 857AN: 1460592Hom.: 13 Cov.: 33 AF XY: 0.000827 AC XY: 601AN XY: 726550 show subpopulations
GnomAD4 exome
AF:
AC:
857
AN:
1460592
Hom.:
Cov.:
33
AF XY:
AC XY:
601
AN XY:
726550
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33474
American (AMR)
AF:
AC:
0
AN:
44684
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26128
East Asian (EAS)
AF:
AC:
0
AN:
39694
South Asian (SAS)
AF:
AC:
704
AN:
86194
European-Finnish (FIN)
AF:
AC:
0
AN:
52554
Middle Eastern (MID)
AF:
AC:
3
AN:
5762
European-Non Finnish (NFE)
AF:
AC:
94
AN:
1111746
Other (OTH)
AF:
AC:
55
AN:
60356
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
47
95
142
190
237
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
20
40
60
80
100
<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: 0.000361 AC: 55AN: 152256Hom.: 0 Cov.: 30 AF XY: 0.000564 AC XY: 42AN XY: 74446 show subpopulations
GnomAD4 genome
AF:
AC:
55
AN:
152256
Hom.:
Cov.:
30
AF XY:
AC XY:
42
AN XY:
74446
show subpopulations
African (AFR)
AF:
AC:
4
AN:
41558
American (AMR)
AF:
AC:
0
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5170
South Asian (SAS)
AF:
AC:
48
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10610
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3
AN:
68010
Other (OTH)
AF:
AC:
0
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.490
Heterozygous variant carriers
0
3
5
8
10
13
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
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
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
13
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV Benign:1
Jan 22, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational 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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