rs16023

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001127222.2(CACNA1A):​c.2975A>T​(p.Glu992Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 1,502,488 control chromosomes in the GnomAD database, including 15,900 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E992Q) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.13 ( 1408 hom., cov: 32)
Exomes 𝑓: 0.14 ( 14492 hom. )

Consequence

CACNA1A
NM_001127222.2 missense

Scores

1
1
16

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:13O:1

Conservation

PhyloP100: 2.84

Publications

22 publications found
Variant links:
Genes affected
CACNA1A (HGNC:1388): (calcium voltage-gated channel subunit alpha1 A) Voltage-dependent calcium channels mediate the entry of calcium ions into excitable cells, and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, and gene expression. Calcium channels are multisubunit complexes composed of alpha-1, beta, alpha-2/delta, and gamma subunits. The channel activity is directed by the pore-forming alpha-1 subunit, whereas, the others act as auxiliary subunits regulating this activity. The distinctive properties of the calcium channel types are related primarily to the expression of a variety of alpha-1 isoforms, alpha-1A, B, C, D, E, and S. This gene encodes the alpha-1A subunit, which is predominantly expressed in neuronal tissue. Mutations in this gene are associated with 2 neurologic disorders, familial hemiplegic migraine and episodic ataxia 2. This gene also exhibits polymorphic variation due to (CAG)n-repeats. Multiple transcript variants encoding different isoforms have been found for this gene. In one set of transcript variants, the (CAG)n-repeats occur in the 3' UTR, and are not associated with any disease. But in another set of variants, an insertion extends the coding region to include the (CAG)n-repeats which encode a polyglutamine tract. Expansion of the (CAG)n-repeats from the normal 4-18 to 21-33 in the coding region is associated with spinocerebellar ataxia 6. [provided by RefSeq, Jul 2016]
CACNA1A Gene-Disease associations (from GenCC):
  • episodic ataxia type 2
    Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
  • undetermined early-onset epileptic encephalopathy
    Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, Illumina
  • developmental and epileptic encephalopathy, 42
    Inheritance: AD Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
  • migraine, familial hemiplegic, 1
    Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
  • spinocerebellar ataxia type 6
    Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Orphanet
  • benign paroxysmal torticollis of infancy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • familial or sporadic hemiplegic migraine
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • Lennox-Gastaut syndrome
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0017878115).
BP6
Variant 19-13298658-T-A is Benign according to our data. Variant chr19-13298658-T-A is described in ClinVar as [Benign]. Clinvar id is 68427.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CACNA1ANM_001127222.2 linkc.2975A>T p.Glu992Val missense_variant Exon 19 of 47 ENST00000360228.11 NP_001120694.1 O00555-8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CACNA1AENST00000360228.11 linkc.2975A>T p.Glu992Val missense_variant Exon 19 of 47 1 NM_001127222.2 ENSP00000353362.5 O00555-8
CACNA1AENST00000638029.1 linkc.2987A>T p.Glu996Val missense_variant Exon 19 of 48 5 ENSP00000489829.1 A0A087WW63
CACNA1AENST00000573710.7 linkc.2981A>T p.Glu994Val missense_variant Exon 19 of 47 5 ENSP00000460092.3 A0A1C7CYY9
CACNA1AENST00000635727.1 linkc.2978A>T p.Glu993Val missense_variant Exon 19 of 47 5 ENSP00000490001.1 A0A1B0GU81
CACNA1AENST00000637769.1 linkc.2978A>T p.Glu993Val missense_variant Exon 19 of 47 1 ENSP00000489778.1 A0A1B0GTN7
CACNA1AENST00000636012.1 linkc.2978A>T p.Glu993Val missense_variant Exon 19 of 46 5 ENSP00000490223.1 A0A1B0GUS3
CACNA1AENST00000637736.1 linkc.2837A>T p.Glu946Val missense_variant Exon 18 of 46 5 ENSP00000489861.1 A0A1B0GTW2
CACNA1AENST00000636389.1 linkc.2978A>T p.Glu993Val missense_variant Exon 19 of 47 5 ENSP00000489992.1 A0A1B0GU74
CACNA1AENST00000637432.1 linkc.2987A>T p.Glu996Val missense_variant Exon 19 of 48 5 ENSP00000490617.1 O00555-2
CACNA1AENST00000636549.1 linkc.2978A>T p.Glu993Val missense_variant Exon 19 of 48 5 ENSP00000490578.1 B5TYJ1
CACNA1AENST00000637927.1 linkc.2981A>T p.Glu994Val missense_variant Exon 19 of 47 5 ENSP00000489715.1 A0A1B0GTI4
CACNA1AENST00000635895.1 linkc.2978A>T p.Glu993Val missense_variant Exon 19 of 47 5 ENSP00000490323.1 A0A384DVW2
CACNA1AENST00000638009.2 linkc.2978A>T p.Glu993Val missense_variant Exon 19 of 47 1 ENSP00000489913.1 O00555-3
CACNA1AENST00000637276.1 linkc.2978A>T p.Glu993Val missense_variant Exon 19 of 46 5 ENSP00000489777.1 O00555-5
CACNA1AENST00000636768.2 linkn.2978A>T non_coding_transcript_exon_variant Exon 19 of 45 5 ENSP00000490190.2 A0A1B0GUP3
CACNA1AENST00000713789.1 linkn.2975A>T non_coding_transcript_exon_variant Exon 19 of 47 ENSP00000519091.1

Frequencies

GnomAD3 genomes
AF:
0.134
AC:
20277
AN:
151782
Hom.:
1410
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.105
Gnomad AMI
AF:
0.163
Gnomad AMR
AF:
0.141
Gnomad ASJ
AF:
0.161
Gnomad EAS
AF:
0.123
Gnomad SAS
AF:
0.120
Gnomad FIN
AF:
0.123
Gnomad MID
AF:
0.182
Gnomad NFE
AF:
0.151
Gnomad OTH
AF:
0.149
GnomAD2 exomes
AF:
0.137
AC:
14100
AN:
102910
AF XY:
0.134
show subpopulations
Gnomad AFR exome
AF:
0.112
Gnomad AMR exome
AF:
0.146
Gnomad ASJ exome
AF:
0.164
Gnomad EAS exome
AF:
0.0934
Gnomad FIN exome
AF:
0.121
Gnomad NFE exome
AF:
0.148
Gnomad OTH exome
AF:
0.177
GnomAD4 exome
AF:
0.144
AC:
194404
AN:
1350598
Hom.:
14492
Cov.:
32
AF XY:
0.144
AC XY:
95757
AN XY:
666138
show subpopulations
African (AFR)
AF:
0.0978
AC:
2641
AN:
27012
American (AMR)
AF:
0.147
AC:
4253
AN:
28944
Ashkenazi Jewish (ASJ)
AF:
0.163
AC:
3820
AN:
23430
East Asian (EAS)
AF:
0.153
AC:
4545
AN:
29706
South Asian (SAS)
AF:
0.116
AC:
8669
AN:
74636
European-Finnish (FIN)
AF:
0.121
AC:
5745
AN:
47320
Middle Eastern (MID)
AF:
0.202
AC:
1109
AN:
5500
European-Non Finnish (NFE)
AF:
0.147
AC:
155295
AN:
1058490
Other (OTH)
AF:
0.150
AC:
8327
AN:
55560
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.473
Heterozygous variant carriers
0
9547
19095
28642
38190
47737
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
5704
11408
17112
22816
28520
<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:
0.133
AC:
20272
AN:
151890
Hom.:
1408
Cov.:
32
AF XY:
0.132
AC XY:
9802
AN XY:
74268
show subpopulations
African (AFR)
AF:
0.104
AC:
4330
AN:
41470
American (AMR)
AF:
0.141
AC:
2145
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.161
AC:
558
AN:
3466
East Asian (EAS)
AF:
0.123
AC:
629
AN:
5130
South Asian (SAS)
AF:
0.120
AC:
578
AN:
4830
European-Finnish (FIN)
AF:
0.123
AC:
1293
AN:
10518
Middle Eastern (MID)
AF:
0.182
AC:
53
AN:
292
European-Non Finnish (NFE)
AF:
0.151
AC:
10226
AN:
67908
Other (OTH)
AF:
0.148
AC:
312
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
937
1873
2810
3746
4683
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
232
464
696
928
1160
<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:
0.145
Hom.:
532
Bravo
AF:
0.135
TwinsUK
AF:
0.138
AC:
512
ALSPAC
AF:
0.146
AC:
563
ESP6500AA
AF:
0.0930
AC:
230
ESP6500EA
AF:
0.128
AC:
655
ExAC
AF:
0.112
AC:
2507
Asia WGS
AF:
0.113
AC:
392
AN:
3466

ClinVar

Significance: Benign
Submissions summary: Benign:13Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:10
Jul 15, 2024
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 30% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 28. Only high quality variants are reported. -

-
Genome Diagnostics Laboratory, University Medical Center Utrecht
Significance:Benign
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

-
PreventionGenetics, part of Exact Sciences
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

-
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Significance:Benign
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

-
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance:Benign
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

-
Genetic Services Laboratory, University of Chicago
Significance:Likely benign
Review Status:no assertion criteria provided
Collection Method:clinical testing

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -

May 03, 2021
Athena Diagnostics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Jan 05, 2016
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Mar 18, 2014
Eurofins Ntd Llc (ga)
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

-
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Significance:Benign
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

not provided Benign:1Other:1
-
UniProtKB/Swiss-Prot
Significance:not provided
Review Status:no classification provided
Collection Method:literature only

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided

- -

Episodic ataxia type 2;C4310716:Developmental and epileptic encephalopathy, 42 Benign:1
Feb 04, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Inborn genetic diseases Benign:1
Mar 11, 2016
Ambry Genetics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.23
BayesDel_addAF
Benign
-0.38
T
BayesDel_noAF
Benign
-0.18
CADD
Benign
22
DANN
Benign
0.91
DEOGEN2
Benign
0.031
.;.;T;.;.;.;.;.;.;T;.;.;.;T;.
Eigen
Benign
-0.31
Eigen_PC
Benign
-0.29
FATHMM_MKL
Benign
0.43
N
LIST_S2
Benign
0.69
T;T;T;T;T;T;T;T;.;T;T;T;T;T;T
MetaRNN
Benign
0.0018
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.61
T
MutationAssessor
Benign
1.1
.;.;.;.;L;.;.;.;.;.;.;.;L;.;.
PhyloP100
2.8
PrimateAI
Pathogenic
0.87
D
PROVEAN
Benign
-1.7
.;N;.;.;.;.;.;.;.;.;.;.;.;.;.
REVEL
Benign
0.28
Sift
Uncertain
0.029
.;D;.;.;.;.;.;.;.;.;.;.;.;.;.
Sift4G
Benign
0.16
T;T;.;.;.;.;.;.;.;.;.;.;.;.;.
Vest4
0.094
MPC
2.0
ClinPred
0.016
T
GERP RS
3.9
Varity_R
0.17
gMVP
0.52
Mutation Taster
=91/9
polymorphism (auto)

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

Other links and lift over

dbSNP: rs16023; hg19: chr19-13409472; COSMIC: COSV64201171; API