12-2053536-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000719.7(CACNA1C):c.-27T>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 0.000000702 in 1,424,352 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000719.7 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1C | ENST00000399603 | c.-27T>G | 5_prime_UTR_variant | Exon 1 of 47 | 5 | NM_001167623.2 | ENSP00000382512.1 | |||
CACNA1C | ENST00000399655 | c.-27T>G | 5_prime_UTR_variant | Exon 1 of 47 | 1 | NM_000719.7 | ENSP00000382563.1 | |||
CACNA1C | ENST00000406454 | c.-27T>G | 5_prime_UTR_variant | Exon 1 of 48 | 5 | ENSP00000385896.3 | ||||
CACNA1C | ENST00000399634 | c.-27T>G | 5_prime_UTR_variant | Exon 1 of 47 | 5 | ENSP00000382542.2 | ||||
CACNA1C | ENST00000347598 | c.-27T>G | 5_prime_UTR_variant | Exon 1 of 49 | 1 | ENSP00000266376.6 | ||||
CACNA1C | ENST00000327702 | c.-27T>G | 5_prime_UTR_variant | Exon 1 of 48 | 1 | ENSP00000329877.7 | ||||
CACNA1C | ENST00000399617 | c.-27T>G | 5_prime_UTR_variant | Exon 1 of 48 | 5 | ENSP00000382526.1 | ||||
CACNA1C | ENST00000335762 | c.-27T>G | 5_prime_UTR_variant | Exon 1 of 48 | 5 | ENSP00000336982.5 | ||||
CACNA1C | ENST00000399641 | c.-27T>G | 5_prime_UTR_variant | Exon 1 of 47 | 1 | ENSP00000382549.1 | ||||
CACNA1C | ENST00000682835 | c.-27T>G | 5_prime_UTR_variant | Exon 1 of 47 | ENSP00000507282.1 | |||||
CACNA1C | ENST00000683482 | c.-27T>G | 5_prime_UTR_variant | Exon 1 of 47 | ENSP00000507169.1 | |||||
CACNA1C | ENST00000682544.1 | c.140-61688T>G | intron_variant | Intron 1 of 49 | ENSP00000507184.1 | |||||
CACNA1C | ENST00000683824.1 | c.140-61688T>G | intron_variant | Intron 1 of 47 | ENSP00000507867.1 | |||||
CACNA1C | ENST00000682462.1 | c.140-61688T>G | intron_variant | Intron 1 of 46 | ENSP00000507105.1 | |||||
CACNA1C | ENST00000683781.1 | c.140-61688T>G | intron_variant | Intron 1 of 46 | ENSP00000507434.1 | |||||
CACNA1C | ENST00000683840.1 | c.140-61688T>G | intron_variant | Intron 1 of 46 | ENSP00000507612.1 | |||||
CACNA1C | ENST00000683956.1 | c.140-61688T>G | intron_variant | Intron 1 of 46 | ENSP00000506882.1 | |||||
CACNA1C | ENST00000344100.7 | c.-27T>G | upstream_gene_variant | 1 | ENSP00000341092.3 | |||||
CACNA1C | ENST00000399638.5 | c.-27T>G | upstream_gene_variant | 1 | ENSP00000382547.1 | |||||
CACNA1C | ENST00000399606.5 | c.-27T>G | upstream_gene_variant | 1 | ENSP00000382515.1 | |||||
CACNA1C | ENST00000399621.5 | c.-27T>G | upstream_gene_variant | 1 | ENSP00000382530.1 | |||||
CACNA1C | ENST00000399637.5 | c.-27T>G | upstream_gene_variant | 1 | ENSP00000382546.1 | |||||
CACNA1C | ENST00000402845.7 | c.-27T>G | upstream_gene_variant | 1 | ENSP00000385724.3 | |||||
CACNA1C | ENST00000399629.5 | c.-27T>G | upstream_gene_variant | 1 | ENSP00000382537.1 | |||||
CACNA1C | ENST00000682336.1 | c.-27T>G | upstream_gene_variant | ENSP00000507898.1 | ||||||
CACNA1C | ENST00000399591.5 | c.-27T>G | upstream_gene_variant | 1 | ENSP00000382500.1 | |||||
CACNA1C | ENST00000399595.5 | c.-27T>G | upstream_gene_variant | 1 | ENSP00000382504.1 | |||||
CACNA1C | ENST00000399649.5 | c.-27T>G | upstream_gene_variant | 1 | ENSP00000382557.1 | |||||
CACNA1C | ENST00000399597.5 | c.-27T>G | upstream_gene_variant | 1 | ENSP00000382506.1 | |||||
CACNA1C | ENST00000399601.5 | c.-27T>G | upstream_gene_variant | 1 | ENSP00000382510.1 | |||||
CACNA1C | ENST00000399644.5 | c.-27T>G | upstream_gene_variant | 1 | ENSP00000382552.1 | |||||
CACNA1C | ENST00000682686.1 | c.-27T>G | upstream_gene_variant | ENSP00000507309.1 | ||||||
CACNA1C | ENST00000480911.6 | n.-27T>G | upstream_gene_variant | 5 | ENSP00000437936.2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000509 AC: 1AN: 196360Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 105716
GnomAD4 exome AF: 7.02e-7 AC: 1AN: 1424352Hom.: 0 Cov.: 33 AF XY: 0.00000142 AC XY: 1AN XY: 705594
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at