12-2053484-TA-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate

The NM_000719.7(CACNA1C):​c.-77delA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: not found (cov: 31)

Consequence

CACNA1C
NM_000719.7 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.276
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 Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 12-2053484-TA-T is Benign according to our data. Variant chr12-2053484-TA-T is described in ClinVar as [Benign]. Clinvar id is 1241429.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CACNA1CNM_000719.7 linkc.-77delA 5_prime_UTR_variant Exon 1 of 47 ENST00000399655.6 NP_000710.5 Q13936-12
CACNA1CNM_001167623.2 linkc.-77delA 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.-77delA 5_prime_UTR_variant Exon 1 of 47 5 NM_001167623.2 ENSP00000382512.1 Q13936-37
CACNA1CENST00000399655 linkc.-77delA 5_prime_UTR_variant Exon 1 of 47 1 NM_000719.7 ENSP00000382563.1 Q13936-12
CACNA1CENST00000406454 linkc.-77delA 5_prime_UTR_variant Exon 1 of 48 5 ENSP00000385896.3 F5GY28
CACNA1CENST00000399634 linkc.-77delA 5_prime_UTR_variant Exon 1 of 47 5 ENSP00000382542.2 E9PDI6
CACNA1CENST00000347598 linkc.-77delA 5_prime_UTR_variant Exon 1 of 49 1 ENSP00000266376.6 Q13936-11
CACNA1CENST00000327702 linkc.-77delA 5_prime_UTR_variant Exon 1 of 48 1 ENSP00000329877.7 A0A0A0MR67
CACNA1CENST00000399617 linkc.-77delA 5_prime_UTR_variant Exon 1 of 48 5 ENSP00000382526.1 A0A0A0MSA1
CACNA1CENST00000335762 linkc.-77delA 5_prime_UTR_variant Exon 1 of 48 5 ENSP00000336982.5 F5H522
CACNA1CENST00000399641 linkc.-77delA 5_prime_UTR_variant Exon 1 of 47 1 ENSP00000382549.1 Q13936-23
CACNA1CENST00000682835 linkc.-77delA 5_prime_UTR_variant Exon 1 of 47 ENSP00000507282.1 A0A804HIZ0
CACNA1CENST00000683482 linkc.-77delA 5_prime_UTR_variant Exon 1 of 47 ENSP00000507169.1 Q13936-35
CACNA1CENST00000682544.1 linkc.140-61738delA intron_variant Intron 1 of 49 ENSP00000507184.1 A0A804HIR0
CACNA1CENST00000683824.1 linkc.140-61738delA intron_variant Intron 1 of 47 ENSP00000507867.1 A0A804HKC4
CACNA1CENST00000682462.1 linkc.140-61738delA intron_variant Intron 1 of 46 ENSP00000507105.1 A0A804HIJ8
CACNA1CENST00000683781.1 linkc.140-61738delA intron_variant Intron 1 of 46 ENSP00000507434.1 A0A804HJB6
CACNA1CENST00000683840.1 linkc.140-61738delA intron_variant Intron 1 of 46 ENSP00000507612.1 A0A804HJR1
CACNA1CENST00000683956.1 linkc.140-61738delA intron_variant Intron 1 of 46 ENSP00000506882.1 A0A804HI37

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
31

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Mar 03, 2015
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-2162650; API