17-50561487-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_018896.5(CACNA1G):c.28G>T(p.Ala10Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000365 in 1,534,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_018896.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1G | ENST00000359106.10 | c.28G>T | p.Ala10Ser | missense_variant | Exon 1 of 38 | 1 | NM_018896.5 | ENSP00000352011.5 | ||
CACNA1G | ENST00000507510.6 | c.28G>T | p.Ala10Ser | missense_variant | Exon 1 of 37 | 1 | ENSP00000423112.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000299 AC: 4AN: 133678Hom.: 0 AF XY: 0.0000547 AC XY: 4AN XY: 73076
GnomAD4 exome AF: 0.0000383 AC: 53AN: 1382860Hom.: 0 Cov.: 32 AF XY: 0.0000381 AC XY: 26AN XY: 682514
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74320
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.28G>T (p.A10S) alteration is located in exon 1 (coding exon 1) of the CACNA1G gene. This alteration results from a G to T substitution at nucleotide position 28, causing the alanine (A) at amino acid position 10 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
CACNA1G: PP2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at