17-66880643-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_145811.3(CACNG5):c.370C>T(p.Arg124Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,614,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R124H) has been classified as Uncertain significance.
Frequency
Consequence
NM_145811.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNG5 | ENST00000533854.6 | c.370C>T | p.Arg124Cys | missense_variant | Exon 4 of 6 | 2 | NM_145811.3 | ENSP00000436836.1 | ||
CACNG5 | ENST00000307139.4 | c.370C>T | p.Arg124Cys | missense_variant | Exon 3 of 5 | 1 | ENSP00000303092.3 | |||
CACNG5 | ENST00000673855.1 | c.370C>T | p.Arg124Cys | missense_variant | Exon 3 of 4 | ENSP00000501267.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251490Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135918
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461836Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727230
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.370C>T (p.R124C) alteration is located in exon 3 (coding exon 3) of the CACNG5 gene. This alteration results from a C to T substitution at nucleotide position 370, causing the arginine (R) at amino acid position 124 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at