rs58173258

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The ENST00000348261.11(CACNA1H):​c.2626G>A​(p.Ala876Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00158 in 1,583,716 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A876V) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0016 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 2 hom. )

Consequence

CACNA1H
ENST00000348261.11 missense

Scores

3
6
10

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2B:3O:2

Conservation

PhyloP100: 1.18
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.01942408).
BP6
Variant 16-1206126-G-A is Benign according to our data. Variant chr16-1206126-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 2706.We mark this variant Likely_benign, oryginal submissions are: {Benign=2, Uncertain_significance=2, not_provided=1}.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00162 (247/152358) while in subpopulation AMR AF= 0.00372 (57/15310). AF 95% confidence interval is 0.00295. There are 0 homozygotes in gnomad4. There are 130 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 247 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CACNA1HNM_021098.3 linkuse as main transcriptc.2626G>A p.Ala876Thr missense_variant 12/35 ENST00000348261.11 NP_066921.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CACNA1HENST00000348261.11 linkuse as main transcriptc.2626G>A p.Ala876Thr missense_variant 12/351 NM_021098.3 ENSP00000334198 P4O95180-1

Frequencies

GnomAD3 genomes
AF:
0.00162
AC:
247
AN:
152240
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000458
Gnomad AMI
AF:
0.0451
Gnomad AMR
AF:
0.00373
Gnomad ASJ
AF:
0.000865
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000658
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00171
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.00117
AC:
236
AN:
201770
Hom.:
0
AF XY:
0.00112
AC XY:
123
AN XY:
109902
show subpopulations
Gnomad AFR exome
AF:
0.000535
Gnomad AMR exome
AF:
0.00255
Gnomad ASJ exome
AF:
0.00142
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000622
Gnomad NFE exome
AF:
0.00136
Gnomad OTH exome
AF:
0.00154
GnomAD4 exome
AF:
0.00158
AC:
2260
AN:
1431358
Hom.:
2
Cov.:
31
AF XY:
0.00148
AC XY:
1048
AN XY:
709606
show subpopulations
Gnomad4 AFR exome
AF:
0.000304
Gnomad4 AMR exome
AF:
0.00260
Gnomad4 ASJ exome
AF:
0.00117
Gnomad4 EAS exome
AF:
0.0000262
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000212
Gnomad4 NFE exome
AF:
0.00183
Gnomad4 OTH exome
AF:
0.00145
GnomAD4 genome
AF:
0.00162
AC:
247
AN:
152358
Hom.:
0
Cov.:
33
AF XY:
0.00174
AC XY:
130
AN XY:
74510
show subpopulations
Gnomad4 AFR
AF:
0.000457
Gnomad4 AMR
AF:
0.00372
Gnomad4 ASJ
AF:
0.000865
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000658
Gnomad4 NFE
AF:
0.00171
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.000482
Hom.:
0
Bravo
AF:
0.00188
TwinsUK
AF:
0.00270
AC:
10
ALSPAC
AF:
0.00208
AC:
8
ESP6500AA
AF:
0.000729
AC:
3
ESP6500EA
AF:
0.00155
AC:
13
ExAC
AF:
0.000835
AC:
99

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:2Benign:3Other:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:1Benign:1
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenApr 01, 2023CACNA1H: BS1, BS2 -
Uncertain significance, criteria provided, single submitterclinical testingAthena DiagnosticsFeb 15, 2021- -
Epilepsy, childhood absence, susceptibility to, 6 Uncertain:1Other:1
not provided, no classification providedphenotyping onlyGenomeConnect - Brain Gene Registry-Variant interpreted as Uncertain significance and reported on 05-31-2019 by Sema4. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Philip Payne PhD, FACMI from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/. -
Uncertain significance, criteria provided, single submitterclinical testingBaylor GeneticsJan 18, 2018This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
CACNA1H-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesApr 11, 2020This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 19, 2024- -
Epilepsy, idiopathic generalized, susceptibility to, 6 Other:1
risk factor, no assertion criteria providedliterature onlyOMIMDec 01, 2007- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.053
T
BayesDel_noAF
Pathogenic
0.15
CADD
Uncertain
23
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.52
D;.;.;.
Eigen
Benign
0.11
Eigen_PC
Benign
0.11
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Uncertain
0.91
D;D;D;.
M_CAP
Pathogenic
0.46
D
MetaRNN
Benign
0.019
T;T;T;T
MetaSVM
Uncertain
0.54
D
MutationAssessor
Benign
1.2
L;.;L;L
MutationTaster
Benign
0.74
N;N;N
PrimateAI
Uncertain
0.59
T
PROVEAN
Benign
-1.5
N;.;N;N
REVEL
Pathogenic
0.66
Sift
Benign
0.55
T;.;T;T
Sift4G
Benign
0.17
T;.;T;T
Polyphen
0.89
P;.;D;D
Vest4
0.35
MVP
0.99
ClinPred
0.036
T
GERP RS
2.9
Varity_R
0.11
gMVP
0.61

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: rs58173258; hg19: chr16-1256126; API