chr12-2607008-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2

The NM_000719.7(CACNA1C):​c.3234C>T​(p.Asp1078Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00096 in 1,613,952 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00098 ( 4 hom. )

Consequence

CACNA1C
NM_000719.7 synonymous

Scores

2

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:8

Conservation

PhyloP100: -2.29
Variant links:
Genes affected
CACNA1C (HGNC:1390): (calcium voltage-gated channel subunit alpha1 C) This gene encodes an alpha-1 subunit of a voltage-dependent calcium channel. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization. The alpha-1 subunit consists of 24 transmembrane segments and forms the pore through which ions pass into the cell. The calcium channel consists of a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. There are multiple isoforms of each of these proteins, either encoded by different genes or the result of alternative splicing of transcripts. The protein encoded by this gene binds to and is inhibited by dihydropyridine. Alternative splicing results in many transcript variants encoding different proteins. Some of the predicted proteins may not produce functional ion channel subunits. [provided by RefSeq, Oct 2012]
CACNA1C-AS3 (HGNC:40117): (CACNA1C antisense RNA 3)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 12-2607008-C-T is Benign according to our data. Variant chr12-2607008-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 195932.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=3, Likely_benign=3}. Variant chr12-2607008-C-T is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-2.29 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000795 (121/152288) while in subpopulation NFE AF= 0.00138 (94/68024). AF 95% confidence interval is 0.00116. There are 0 homozygotes in gnomad4. There are 57 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 121 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CACNA1CNM_000719.7 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 ENST00000399655.6 NP_000710.5 Q13936-12
CACNA1CNM_001167623.2 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 ENST00000399603.6 NP_001161095.1 Q13936-37

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CACNA1CENST00000399603.6 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 5 NM_001167623.2 ENSP00000382512.1 Q13936-37
CACNA1CENST00000399655.6 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 1 NM_000719.7 ENSP00000382563.1 Q13936-12
CACNA1CENST00000682544.1 linkc.3384C>T p.Asp1128Asp synonymous_variant Exon 27 of 50 ENSP00000507184.1 A0A804HIR0
CACNA1CENST00000406454.8 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 48 5 ENSP00000385896.3 F5GY28
CACNA1CENST00000399634.6 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 5 ENSP00000382542.2 E9PDI6
CACNA1CENST00000683824.1 linkc.3399C>T p.Asp1133Asp synonymous_variant Exon 27 of 48 ENSP00000507867.1 A0A804HKC4
CACNA1CENST00000347598.9 linkc.3294C>T p.Asp1098Asp synonymous_variant Exon 27 of 49 1 ENSP00000266376.6 Q13936-11
CACNA1CENST00000344100.7 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 1 ENSP00000341092.3 Q13936-14
CACNA1CENST00000327702.12 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 48 1 ENSP00000329877.7 A0A0A0MR67
CACNA1CENST00000399617.6 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 48 5 ENSP00000382526.1 A0A0A0MSA1
CACNA1CENST00000682462.1 linkc.3324C>T p.Asp1108Asp synonymous_variant Exon 26 of 47 ENSP00000507105.1 A0A804HIJ8
CACNA1CENST00000683781.1 linkc.3324C>T p.Asp1108Asp synonymous_variant Exon 26 of 47 ENSP00000507434.1 A0A804HJB6
CACNA1CENST00000683840.1 linkc.3324C>T p.Asp1108Asp synonymous_variant Exon 26 of 47 ENSP00000507612.1 A0A804HJR1
CACNA1CENST00000683956.1 linkc.3324C>T p.Asp1108Asp synonymous_variant Exon 26 of 47 ENSP00000506882.1 A0A804HI37
CACNA1CENST00000399638.5 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 48 1 ENSP00000382547.1 Q13936-31
CACNA1CENST00000335762.10 linkc.3309C>T p.Asp1103Asp synonymous_variant Exon 27 of 48 5 ENSP00000336982.5 F5H522
CACNA1CENST00000399606.5 linkc.3294C>T p.Asp1098Asp synonymous_variant Exon 27 of 48 1 ENSP00000382515.1 Q13936-30
CACNA1CENST00000399621.5 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 1 ENSP00000382530.1 Q13936-24
CACNA1CENST00000399637.5 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 1 ENSP00000382546.1 Q13936-27
CACNA1CENST00000402845.7 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 1 ENSP00000385724.3 Q13936-13
CACNA1CENST00000399629.5 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 1 ENSP00000382537.1 Q13936-32
CACNA1CENST00000682336.1 linkc.3309C>T p.Asp1103Asp synonymous_variant Exon 27 of 47 ENSP00000507898.1 A0A804HKE9
CACNA1CENST00000399591.5 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 46 1 ENSP00000382500.1 Q13936-29
CACNA1CENST00000399595.5 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 46 1 ENSP00000382504.1 Q13936-25
CACNA1CENST00000399649.5 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 46 1 ENSP00000382557.1 Q13936-15
CACNA1CENST00000399597.5 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 1 ENSP00000382506.1 Q13936-22
CACNA1CENST00000399601.5 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 1 ENSP00000382510.1 Q13936-20
CACNA1CENST00000399641.6 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 1 ENSP00000382549.1 Q13936-23
CACNA1CENST00000399644.5 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 1 ENSP00000382552.1 Q13936-21
CACNA1CENST00000682835.1 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 47 ENSP00000507282.1 A0A804HIZ0
CACNA1CENST00000683482.1 linkc.3225C>T p.Asp1075Asp synonymous_variant Exon 26 of 47 ENSP00000507169.1 Q13936-35
CACNA1CENST00000682686.1 linkc.3234C>T p.Asp1078Asp synonymous_variant Exon 26 of 46 ENSP00000507309.1 Q13936-19
CACNA1CENST00000480911.6 linkn.*1841C>T non_coding_transcript_exon_variant Exon 24 of 27 5 ENSP00000437936.2 F5H638
CACNA1CENST00000480911.6 linkn.*1841C>T 3_prime_UTR_variant Exon 24 of 27 5 ENSP00000437936.2 F5H638

Frequencies

GnomAD3 genomes
AF:
0.000795
AC:
121
AN:
152170
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000327
Gnomad ASJ
AF:
0.00432
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.000377
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00138
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000867
AC:
216
AN:
249226
Hom.:
2
AF XY:
0.000865
AC XY:
117
AN XY:
135214
show subpopulations
Gnomad AFR exome
AF:
0.0000646
Gnomad AMR exome
AF:
0.000203
Gnomad ASJ exome
AF:
0.00397
Gnomad EAS exome
AF:
0.000111
Gnomad SAS exome
AF:
0.0000654
Gnomad FIN exome
AF:
0.000650
Gnomad NFE exome
AF:
0.00127
Gnomad OTH exome
AF:
0.000991
GnomAD4 exome
AF:
0.000978
AC:
1429
AN:
1461664
Hom.:
4
Cov.:
31
AF XY:
0.00102
AC XY:
745
AN XY:
727120
show subpopulations
Gnomad4 AFR exome
AF:
0.0000896
Gnomad4 AMR exome
AF:
0.000201
Gnomad4 ASJ exome
AF:
0.00325
Gnomad4 EAS exome
AF:
0.0000756
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.000487
Gnomad4 NFE exome
AF:
0.00112
Gnomad4 OTH exome
AF:
0.000944
GnomAD4 genome
AF:
0.000795
AC:
121
AN:
152288
Hom.:
0
Cov.:
33
AF XY:
0.000765
AC XY:
57
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.000327
Gnomad4 ASJ
AF:
0.00432
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.000377
Gnomad4 NFE
AF:
0.00138
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.00134
Hom.:
0
Bravo
AF:
0.000752
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.00136
EpiControl
AF:
0.000889

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:8
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:1Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxMar 03, 2015- -
Uncertain significance, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Sep 29, 2015- -
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJul 01, 2024CACNA1C: BP4, BP7, BS1 -
not specified Benign:3
Benign, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpMar 25, 2021- -
Benign, no assertion criteria providedclinical testingClinical Genetics, Academic Medical Center-- -
Benign, no assertion criteria providedclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Timothy syndrome;C2678478:Brugada syndrome 3;C5774213:Neurodevelopmental disorder with hypotonia, language delay, and skeletal defects with or without seizures;CN260585:Long qt syndrome 8 Benign:1
Likely benign, criteria provided, single submitterclinical testingCenter for Genomics, Ann and Robert H. Lurie Children's Hospital of ChicagoJul 25, 2022This variant has not been reported in the literature but is present in the Genome Aggregation Database (Highest reported MAF: 0.4% [41/10356] including 2 total homozygotes; https://gnomad.broadinstitute.org/variant/12-2716174-C-T?dataset=gnomad_r2_1). This variant is present in ClinVar (Variation ID:195932). Of note, this variant is a silent variant and does not change the amino acid, is not predicted to impact splicing, and this nucleotide position is poorly conserved evolutionarily, reducing the probability that this variant is disease-causing. In summary, data on this variant suggests that this variant does not cause disease but requires further evidence. Therefore, this variant is classified as likely benign. -
Long QT syndrome Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 03, 2025- -
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitterclinical testingAmbry GeneticsMay 18, 2015This alteration is classified as likely 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
BayesDel_noAF
Benign
-0.34
CADD
Benign
4.1
DANN
Benign
0.82

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs111606207; hg19: chr12-2716174; API