rs139052540
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006078.5(CACNG2):c.640G>A(p.Ala214Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00063 in 1,613,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_006078.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNG2 | NM_006078.5 | c.640G>A | p.Ala214Thr | missense_variant | Exon 4 of 4 | ENST00000300105.7 | NP_006069.1 | |
CACNG2 | NM_001379051.1 | c.571G>A | p.Ala191Thr | missense_variant | Exon 5 of 5 | NP_001365980.1 | ||
CACNG2 | XM_017028531.3 | c.382G>A | p.Ala128Thr | missense_variant | Exon 3 of 3 | XP_016884020.1 | ||
CACNG2 | NR_166440.1 | n.2006G>A | non_coding_transcript_exon_variant | Exon 5 of 5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000532 AC: 81AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000458 AC: 115AN: 250918Hom.: 0 AF XY: 0.000413 AC XY: 56AN XY: 135720
GnomAD4 exome AF: 0.000640 AC: 936AN: 1461674Hom.: 0 Cov.: 33 AF XY: 0.000583 AC XY: 424AN XY: 727152
GnomAD4 genome AF: 0.000532 AC: 81AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
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not provided Uncertain:1
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CACNG2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at