16-1153321-CGGGCCGGGGGCGGAGGCGCTGGGGGCCGGGGCCG-C
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_021098.3(CACNA1H):c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 139,872 control chromosomes in the GnomAD database, including 2,056 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 2053 hom., cov: 21)
Exomes 𝑓: 0.092 ( 3 hom. )
Consequence
CACNA1H
NM_021098.3 5_prime_UTR
NM_021098.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.12
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]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP6
Variant 16-1153321-CGGGCCGGGGGCGGAGGCGCTGGGGGCCGGGGCCG-C is Benign according to our data. Variant chr16-1153321-CGGGCCGGGGGCGGAGGCGCTGGGGGCCGGGGCCG-C is described in ClinVar as [Benign]. Clinvar id is 1275909.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CACNA1H | ENST00000348261.11 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | 1 | NM_021098.3 | ENSP00000334198.7 | |||
| CACNA1H | ENST00000569107.6 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | 1 | ENSP00000454990.2 | ||||
| CACNA1H | ENST00000711493.1 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | ENSP00000518778.1 | |||||
| CACNA1H | ENST00000565831.7 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | 1 | ENSP00000455840.1 | ||||
| CACNA1H | ENST00000711450.1 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | ENSP00000518762.1 | |||||
| CACNA1H | ENST00000564231.6 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | 1 | ENSP00000457555.2 | ||||
| CACNA1H | ENST00000638323.1 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | 5 | ENSP00000492267.1 | ||||
| CACNA1H | ENST00000562079.6 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | 1 | ENSP00000454581.2 | ||||
| CACNA1H | ENST00000711438.1 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | ENSP00000518754.1 | |||||
| CACNA1H | ENST00000711482.1 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518771.1 | |||||
| CACNA1H | ENST00000711485.1 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | ENSP00000518774.1 | |||||
| CACNA1H | ENST00000711455.1 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518768.1 | |||||
| CACNA1H | ENST00000711483.1 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | ENSP00000518772.1 | |||||
| CACNA1H | ENST00000711456.1 | c.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | ENSP00000518769.1 | |||||
| CACNA1H | ENST00000621827.2 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 37 | 6 | ENSP00000518766.1 | ||||
| CACNA1H | ENST00000637236.3 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 34 | 5 | ENSP00000492650.2 | ||||
| CACNA1H | ENST00000639478.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 35 | 5 | ENSP00000491945.1 | ||||
| CACNA1H | ENST00000640028.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 35 | 5 | ENSP00000491488.1 | ||||
| CACNA1H | ENST00000711442.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 34 | ENSP00000518758.1 | |||||
| CACNA1H | ENST00000711448.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 36 | ENSP00000518760.1 | |||||
| CACNA1H | ENST00000711449.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 35 | ENSP00000518761.1 | |||||
| CACNA1H | ENST00000711451.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 36 | ENSP00000518763.1 | |||||
| CACNA1H | ENST00000711452.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 36 | ENSP00000518764.1 | |||||
| CACNA1H | ENST00000711453.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 36 | ENSP00000518765.1 | |||||
| CACNA1H | ENST00000711484.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 35 | ENSP00000518773.1 | |||||
| CACNA1H | ENST00000711486.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 37 | ENSP00000518775.1 | |||||
| CACNA1H | ENST00000711487.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 36 | ENSP00000518776.1 | |||||
| CACNA1H | ENST00000711488.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | non_coding_transcript_exon_variant | Exon 1 of 35 | ENSP00000518777.1 | |||||
| CACNA1H | ENST00000621827.2 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 37 | 6 | ENSP00000518766.1 | ||||
| CACNA1H | ENST00000637236.3 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | 5 | ENSP00000492650.2 | ||||
| CACNA1H | ENST00000639478.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | 5 | ENSP00000491945.1 | ||||
| CACNA1H | ENST00000640028.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | 5 | ENSP00000491488.1 | ||||
| CACNA1H | ENST00000711442.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 34 | ENSP00000518758.1 | |||||
| CACNA1H | ENST00000711448.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518760.1 | |||||
| CACNA1H | ENST00000711449.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | ENSP00000518761.1 | |||||
| CACNA1H | ENST00000711451.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518763.1 | |||||
| CACNA1H | ENST00000711452.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518764.1 | |||||
| CACNA1H | ENST00000711453.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518765.1 | |||||
| CACNA1H | ENST00000711484.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | ENSP00000518773.1 | |||||
| CACNA1H | ENST00000711486.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 37 | ENSP00000518775.1 | |||||
| CACNA1H | ENST00000711487.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 36 | ENSP00000518776.1 | |||||
| CACNA1H | ENST00000711488.1 | n.-125_-92delGGCGGAGGCGCTGGGGGCCGGGGCCGGGGCCGGG | 5_prime_UTR_variant | Exon 1 of 35 | ENSP00000518777.1 | |||||
| CACNA1H | ENST00000711438.1 | c.-167_-134delGGGCCGGGGGCGGAGGCGCTGGGGGCCGGGGCCG | upstream_gene_variant | ENSP00000518754.1 |
Frequencies
GnomAD3 genomes 0.163 AC: 22743AN: 139256Hom.: 2050 Cov.: 21 show subpopulations
GnomAD3 genomes
AF:
AC:
22743
AN:
139256
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
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0918 AC: 56AN: 610Hom.: 3 AF XY: 0.0972 AC XY: 28AN XY: 288 show subpopulations
GnomAD4 exome
AF:
AC:
56
AN:
610
Hom.:
AF XY:
AC XY:
28
AN XY:
288
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
AC:
55
AN:
606
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AF:
AC:
1
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.413
Heterozygous variant carriers
0
3
6
9
12
15
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.163 AC: 22744AN: 139262Hom.: 2053 Cov.: 21 AF XY: 0.158 AC XY: 10689AN XY: 67706 show subpopulations
GnomAD4 genome
AF:
AC:
22744
AN:
139262
Hom.:
Cov.:
21
AF XY:
AC XY:
10689
AN XY:
67706
show subpopulations
African (AFR)
AF:
AC:
4482
AN:
38500
American (AMR)
AF:
AC:
2211
AN:
14326
Ashkenazi Jewish (ASJ)
AF:
AC:
788
AN:
3342
East Asian (EAS)
AF:
AC:
327
AN:
4454
South Asian (SAS)
AF:
AC:
512
AN:
4344
European-Finnish (FIN)
AF:
AC:
1177
AN:
7754
Middle Eastern (MID)
AF:
AC:
32
AN:
244
European-Non Finnish (NFE)
AF:
AC:
12856
AN:
63488
Other (OTH)
AF:
AC:
331
AN:
1938
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.447
Heterozygous variant carriers
0
858
1716
2573
3431
4289
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 04, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational 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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