chr12-2053561-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_000719.7(CACNA1C):​c.-2C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,222 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CACNA1C
NM_000719.7 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.293
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CACNA1CNM_000719.7 linkc.-2C>G 5_prime_UTR_variant Exon 1 of 47 ENST00000399655.6 NP_000710.5 Q13936-12
CACNA1CNM_001167623.2 linkc.-2C>G 5_prime_UTR_variant Exon 1 of 47 ENST00000399603.6 NP_001161095.1 Q13936-37

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CACNA1CENST00000399603 linkc.-2C>G 5_prime_UTR_variant Exon 1 of 47 5 NM_001167623.2 ENSP00000382512.1 Q13936-37
CACNA1CENST00000399655 linkc.-2C>G 5_prime_UTR_variant Exon 1 of 47 1 NM_000719.7 ENSP00000382563.1 Q13936-12
CACNA1CENST00000406454 linkc.-2C>G 5_prime_UTR_variant Exon 1 of 48 5 ENSP00000385896.3 F5GY28
CACNA1CENST00000399634 linkc.-2C>G 5_prime_UTR_variant Exon 1 of 47 5 ENSP00000382542.2 E9PDI6
CACNA1CENST00000347598 linkc.-2C>G 5_prime_UTR_variant Exon 1 of 49 1 ENSP00000266376.6 Q13936-11
CACNA1CENST00000327702 linkc.-2C>G 5_prime_UTR_variant Exon 1 of 48 1 ENSP00000329877.7 A0A0A0MR67
CACNA1CENST00000399617 linkc.-2C>G 5_prime_UTR_variant Exon 1 of 48 5 ENSP00000382526.1 A0A0A0MSA1
CACNA1CENST00000335762 linkc.-2C>G 5_prime_UTR_variant Exon 1 of 48 5 ENSP00000336982.5 F5H522
CACNA1CENST00000399641 linkc.-2C>G 5_prime_UTR_variant Exon 1 of 47 1 ENSP00000382549.1 Q13936-23
CACNA1CENST00000682835 linkc.-2C>G 5_prime_UTR_variant Exon 1 of 47 ENSP00000507282.1 A0A804HIZ0
CACNA1CENST00000683482 linkc.-2C>G 5_prime_UTR_variant Exon 1 of 47 ENSP00000507169.1 Q13936-35
CACNA1CENST00000682544.1 linkc.140-61663C>G intron_variant Intron 1 of 49 ENSP00000507184.1 A0A804HIR0
CACNA1CENST00000683824.1 linkc.140-61663C>G intron_variant Intron 1 of 47 ENSP00000507867.1 A0A804HKC4
CACNA1CENST00000682462.1 linkc.140-61663C>G intron_variant Intron 1 of 46 ENSP00000507105.1 A0A804HIJ8
CACNA1CENST00000683781.1 linkc.140-61663C>G intron_variant Intron 1 of 46 ENSP00000507434.1 A0A804HJB6
CACNA1CENST00000683840.1 linkc.140-61663C>G intron_variant Intron 1 of 46 ENSP00000507612.1 A0A804HJR1
CACNA1CENST00000683956.1 linkc.140-61663C>G intron_variant Intron 1 of 46 ENSP00000506882.1 A0A804HI37
CACNA1CENST00000480911.6 linkn.-2C>G non_coding_transcript_exon_variant Exon 1 of 27 5 ENSP00000437936.2 F5H638
CACNA1CENST00000480911.6 linkn.-2C>G 5_prime_UTR_variant Exon 1 of 27 5 ENSP00000437936.2 F5H638
CACNA1CENST00000344100.7 linkc.-2C>G upstream_gene_variant 1 ENSP00000341092.3 Q13936-14
CACNA1CENST00000399638.5 linkc.-2C>G upstream_gene_variant 1 ENSP00000382547.1 Q13936-31
CACNA1CENST00000399606.5 linkc.-2C>G upstream_gene_variant 1 ENSP00000382515.1 Q13936-30
CACNA1CENST00000399621.5 linkc.-2C>G upstream_gene_variant 1 ENSP00000382530.1 Q13936-24
CACNA1CENST00000399637.5 linkc.-2C>G upstream_gene_variant 1 ENSP00000382546.1 Q13936-27
CACNA1CENST00000402845.7 linkc.-2C>G upstream_gene_variant 1 ENSP00000385724.3 Q13936-13
CACNA1CENST00000399629.5 linkc.-2C>G upstream_gene_variant 1 ENSP00000382537.1 Q13936-32
CACNA1CENST00000682336.1 linkc.-2C>G upstream_gene_variant ENSP00000507898.1 A0A804HKE9
CACNA1CENST00000399591.5 linkc.-2C>G upstream_gene_variant 1 ENSP00000382500.1 Q13936-29
CACNA1CENST00000399595.5 linkc.-2C>G upstream_gene_variant 1 ENSP00000382504.1 Q13936-25
CACNA1CENST00000399649.5 linkc.-2C>G upstream_gene_variant 1 ENSP00000382557.1 Q13936-15
CACNA1CENST00000399597.5 linkc.-2C>G upstream_gene_variant 1 ENSP00000382506.1 Q13936-22
CACNA1CENST00000399601.5 linkc.-2C>G upstream_gene_variant 1 ENSP00000382510.1 Q13936-20
CACNA1CENST00000399644.5 linkc.-2C>G upstream_gene_variant 1 ENSP00000382552.1 Q13936-21
CACNA1CENST00000682686.1 linkc.-2C>G upstream_gene_variant ENSP00000507309.1 Q13936-19

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152104
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000457
AC:
1
AN:
219036
Hom.:
0
AF XY:
0.00000845
AC XY:
1
AN XY:
118328
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000377
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1442160
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
715572
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152222
Hom.:
0
Cov.:
31
AF XY:
0.0000134
AC XY:
1
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
CADD
Benign
17
DANN
Benign
0.82

Splicing

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: rs536361695; hg19: chr12-2162727; API