12-2053203-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000719.7(CACNA1C):c.-360G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,000,742 control chromosomes in the GnomAD database, including 14,884 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000719.7 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1C | ENST00000399603 | c.-360G>A | 5_prime_UTR_variant | Exon 1 of 47 | 5 | NM_001167623.2 | ENSP00000382512.1 | |||
CACNA1C | ENST00000399655 | c.-360G>A | 5_prime_UTR_variant | Exon 1 of 47 | 1 | NM_000719.7 | ENSP00000382563.1 | |||
CACNA1C | ENST00000406454 | c.-360G>A | 5_prime_UTR_variant | Exon 1 of 48 | 5 | ENSP00000385896.3 | ||||
CACNA1C | ENST00000399634 | c.-360G>A | 5_prime_UTR_variant | Exon 1 of 47 | 5 | ENSP00000382542.2 | ||||
CACNA1C | ENST00000347598 | c.-360G>A | 5_prime_UTR_variant | Exon 1 of 49 | 1 | ENSP00000266376.6 | ||||
CACNA1C | ENST00000327702 | c.-360G>A | 5_prime_UTR_variant | Exon 1 of 48 | 1 | ENSP00000329877.7 | ||||
CACNA1C | ENST00000335762 | c.-360G>A | 5_prime_UTR_variant | Exon 1 of 48 | 5 | ENSP00000336982.5 | ||||
CACNA1C | ENST00000399641 | c.-360G>A | 5_prime_UTR_variant | Exon 1 of 47 | 1 | ENSP00000382549.1 | ||||
CACNA1C | ENST00000682835 | c.-360G>A | 5_prime_UTR_variant | Exon 1 of 47 | ENSP00000507282.1 | |||||
CACNA1C | ENST00000682544.1 | c.140-62021G>A | intron_variant | Intron 1 of 49 | ENSP00000507184.1 | |||||
CACNA1C | ENST00000683824.1 | c.140-62021G>A | intron_variant | Intron 1 of 47 | ENSP00000507867.1 | |||||
CACNA1C | ENST00000682462.1 | c.140-62021G>A | intron_variant | Intron 1 of 46 | ENSP00000507105.1 | |||||
CACNA1C | ENST00000683781.1 | c.140-62021G>A | intron_variant | Intron 1 of 46 | ENSP00000507434.1 | |||||
CACNA1C | ENST00000683840.1 | c.140-62021G>A | intron_variant | Intron 1 of 46 | ENSP00000507612.1 | |||||
CACNA1C | ENST00000683956.1 | c.140-62021G>A | intron_variant | Intron 1 of 46 | ENSP00000506882.1 |
Frequencies
GnomAD3 genomes AF: 0.172 AC: 26000AN: 151546Hom.: 2316 Cov.: 31
GnomAD4 exome AF: 0.172 AC: 146077AN: 849084Hom.: 12568 Cov.: 31 AF XY: 0.172 AC XY: 67534AN XY: 393368
GnomAD4 genome AF: 0.172 AC: 26018AN: 151658Hom.: 2316 Cov.: 31 AF XY: 0.172 AC XY: 12766AN XY: 74110
ClinVar
Submissions by phenotype
not provided Benign:2
- -
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