rs201985877
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_006030.4(CACNA2D2):āc.1392A>Gā(p.Glu464=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000633 in 1,610,972 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_006030.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA2D2 | NM_006030.4 | c.1392A>G | p.Glu464= | splice_region_variant, synonymous_variant | 15/38 | ENST00000424201.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA2D2 | ENST00000424201.7 | c.1392A>G | p.Glu464= | splice_region_variant, synonymous_variant | 15/38 | 1 | NM_006030.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152126Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000370 AC: 92AN: 248338Hom.: 1 AF XY: 0.000327 AC XY: 44AN XY: 134654
GnomAD4 exome AF: 0.0000658 AC: 96AN: 1458726Hom.: 1 Cov.: 32 AF XY: 0.0000648 AC XY: 47AN XY: 725784
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74462
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at