rs797045426
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS2
The NM_006078.5(CACNG2):c.437-7C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,457,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006078.5 splice_region, intron
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNG2 | NM_006078.5 | c.437-7C>A | splice_region_variant, intron_variant | ENST00000300105.7 | NP_006069.1 | |||
CACNG2 | NM_001379051.1 | c.368-7C>A | splice_region_variant, intron_variant | NP_001365980.1 | ||||
CACNG2 | XM_017028531.3 | c.179-7C>A | splice_region_variant, intron_variant | XP_016884020.1 | ||||
CACNG2 | NR_166440.1 | n.1803-7C>A | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNG2 | ENST00000300105.7 | c.437-7C>A | splice_region_variant, intron_variant | 1 | NM_006078.5 | ENSP00000300105.6 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000826 AC: 2AN: 242018Hom.: 0 AF XY: 0.00000757 AC XY: 1AN XY: 132112
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1457432Hom.: 0 Cov.: 33 AF XY: 0.00000414 AC XY: 3AN XY: 725228
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 09, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at