19-53993190-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_145814.2(CACNG6):c.313C>T(p.Pro105Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000144 in 1,389,414 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P105L) has been classified as Uncertain significance.
Frequency
Consequence
NM_145814.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNG6 | NM_145814.2 | c.313C>T | p.Pro105Ser | missense_variant | Exon 1 of 4 | ENST00000252729.7 | NP_665813.1 | |
CACNG6 | NM_145815.2 | c.313C>T | p.Pro105Ser | missense_variant | Exon 1 of 3 | NP_665814.1 | ||
CACNG6 | NM_031897.3 | c.313C>T | p.Pro105Ser | missense_variant | Exon 1 of 2 | NP_114103.2 | ||
CACNG6 | NR_102308.2 | n.49+1993C>T | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNG6 | ENST00000252729.7 | c.313C>T | p.Pro105Ser | missense_variant | Exon 1 of 4 | 1 | NM_145814.2 | ENSP00000252729.2 | ||
CACNG6 | ENST00000346968.2 | c.313C>T | p.Pro105Ser | missense_variant | Exon 1 of 3 | 5 | ENSP00000319097.2 | |||
CACNG6 | ENST00000352529.1 | c.313C>T | p.Pro105Ser | missense_variant | Exon 1 of 2 | 5 | ENSP00000319135.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000152 AC: 2AN: 131370Hom.: 0 AF XY: 0.0000139 AC XY: 1AN XY: 71714
GnomAD4 exome AF: 0.00000144 AC: 2AN: 1389414Hom.: 0 Cov.: 31 AF XY: 0.00000292 AC XY: 2AN XY: 685572
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.313C>T (p.P105S) alteration is located in exon 1 (coding exon 1) of the CACNG6 gene. This alteration results from a C to T substitution at nucleotide position 313, causing the proline (P) at amino acid position 105 to be replaced by a serine (S). 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