16-1153321-C-CGGGCCGGGGGCGGAGGCGCTGGGGGCCGGGGCCG
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2
The ENST00000711486.1(CACNA1H):n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000186 in 139,544 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., cov: 21)
Consequence
CACNA1H
ENST00000711486.1 non_coding_transcript_exon
ENST00000711486.1 non_coding_transcript_exon
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.64
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 -8 ACMG points.
BS1
Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.000186 (26/139544) while in subpopulation EAS AF = 0.000897 (4/4460). AF 95% confidence interval is 0.000306. There are 0 homozygotes in GnomAd4. There are 16 alleles in the male GnomAd4 subpopulation. Median coverage is 21. This position passed quality control check.
BS2
High AC in GnomAd4 at 26 AD gene.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CACNA1H | ENST00000621827.2 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 37 | 6 | ENSP00000518766.1 | ||||
| CACNA1H | ENST00000637236.3 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 34 | 5 | ENSP00000492650.2 | ||||
| CACNA1H | ENST00000639478.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 35 | 5 | ENSP00000491945.1 | ||||
| CACNA1H | ENST00000640028.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 35 | 5 | ENSP00000491488.1 | ||||
| CACNA1H | ENST00000711442.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 34 | ENSP00000518758.1 | |||||
| CACNA1H | ENST00000711448.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 36 | ENSP00000518760.1 | |||||
| CACNA1H | ENST00000711449.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 35 | ENSP00000518761.1 | |||||
| CACNA1H | ENST00000711451.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 36 | ENSP00000518763.1 | |||||
| CACNA1H | ENST00000711452.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 36 | ENSP00000518764.1 | |||||
| CACNA1H | ENST00000711453.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 36 | ENSP00000518765.1 | |||||
| CACNA1H | ENST00000711484.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 35 | ENSP00000518773.1 | |||||
| CACNA1H | ENST00000711486.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 37 | ENSP00000518775.1 | |||||
| CACNA1H | ENST00000711487.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 36 | ENSP00000518776.1 | |||||
| CACNA1H | ENST00000711488.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 35 | ENSP00000518777.1 | |||||
| CACNA1H | ENST00000348261.11 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | 1 | NM_021098.3 | ENSP00000334198.7 | |||
| CACNA1H | ENST00000569107.6 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | 1 | ENSP00000454990.2 | ||||
| CACNA1H | ENST00000711493.1 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | ENSP00000518778.1 | |||||
| CACNA1H | ENST00000565831.7 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | 1 | ENSP00000455840.1 | ||||
| CACNA1H | ENST00000711450.1 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | ENSP00000518762.1 | |||||
| CACNA1H | ENST00000564231.6 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | 1 | ENSP00000457555.2 | ||||
| CACNA1H | ENST00000638323.1 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | 5 | ENSP00000492267.1 | ||||
| CACNA1H | ENST00000562079.6 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | 1 | ENSP00000454581.2 | ||||
| CACNA1H | ENST00000711438.1 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | ENSP00000518754.1 | |||||
| CACNA1H | ENST00000711482.1 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518771.1 | |||||
| CACNA1H | ENST00000711485.1 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | ENSP00000518774.1 | |||||
| CACNA1H | ENST00000711455.1 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518768.1 | |||||
| CACNA1H | ENST00000711483.1 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | ENSP00000518772.1 | |||||
| CACNA1H | ENST00000711456.1 | c.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | ENSP00000518769.1 | |||||
| CACNA1H | ENST00000621827.2 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 37 | 6 | ENSP00000518766.1 | ||||
| CACNA1H | ENST00000637236.3 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | 5 | ENSP00000492650.2 | ||||
| CACNA1H | ENST00000639478.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | 5 | ENSP00000491945.1 | ||||
| CACNA1H | ENST00000640028.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | 5 | ENSP00000491488.1 | ||||
| CACNA1H | ENST00000711442.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | ENSP00000518758.1 | |||||
| CACNA1H | ENST00000711448.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518760.1 | |||||
| CACNA1H | ENST00000711449.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | ENSP00000518761.1 | |||||
| CACNA1H | ENST00000711451.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518763.1 | |||||
| CACNA1H | ENST00000711452.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518764.1 | |||||
| CACNA1H | ENST00000711453.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518765.1 | |||||
| CACNA1H | ENST00000711484.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | ENSP00000518773.1 | |||||
| CACNA1H | ENST00000711486.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 37 | ENSP00000518775.1 | |||||
| CACNA1H | ENST00000711487.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518776.1 | |||||
| CACNA1H | ENST00000711488.1 | n.-125_-92dupGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | ENSP00000518777.1 | |||||
| CACNA1H | ENST00000711438.1 | c.-168_-167insGGGCCGGGGGCGGAGGCGCTGGGGGCCGGGGCCG | upstream_gene_variant | ENSP00000518754.1 |
Frequencies
GnomAD3 genomes 0.000186 AC: 26AN: 139540Hom.: 0 Cov.: 21 show subpopulations
GnomAD3 genomes
AF:
AC:
26
AN:
139540
Hom.:
Cov.:
21
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
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Gnomad OTH
AF:
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
GnomAD4 genome 0.000186 AC: 26AN: 139544Hom.: 0 Cov.: 21 AF XY: 0.000236 AC XY: 16AN XY: 67840 show subpopulations
GnomAD4 genome
AF:
AC:
26
AN:
139544
Hom.:
Cov.:
21
AF XY:
AC XY:
16
AN XY:
67840
show subpopulations
African (AFR)
AF:
AC:
18
AN:
38574
American (AMR)
AF:
AC:
1
AN:
14340
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3344
East Asian (EAS)
AF:
AC:
4
AN:
4460
South Asian (SAS)
AF:
AC:
0
AN:
4354
European-Finnish (FIN)
AF:
AC:
1
AN:
7770
Middle Eastern (MID)
AF:
AC:
0
AN:
244
European-Non Finnish (NFE)
AF:
AC:
2
AN:
63646
Other (OTH)
AF:
AC:
0
AN:
1940
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.550
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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