chr19-13208785-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP6BS2
The NM_001127222.2(CACNA1A):c.6751G>A(p.Glu2251Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000148 in 1,553,364 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E2251G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001127222.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1A | NM_001127222.2 | c.6751G>A | p.Glu2251Lys | missense_variant | 46/47 | ENST00000360228.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1A | ENST00000360228.11 | c.6751G>A | p.Glu2251Lys | missense_variant | 46/47 | 1 | NM_001127222.2 |
Frequencies
GnomAD3 genomes AF: 0.0000468 AC: 7AN: 149708Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000113 AC: 2AN: 176608Hom.: 0 AF XY: 0.0000102 AC XY: 1AN XY: 98390
GnomAD4 exome AF: 0.0000114 AC: 16AN: 1403656Hom.: 0 Cov.: 33 AF XY: 0.0000129 AC XY: 9AN XY: 695710
GnomAD4 genome AF: 0.0000468 AC: 7AN: 149708Hom.: 0 Cov.: 31 AF XY: 0.0000410 AC XY: 3AN XY: 73110
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jan 19, 2021 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Episodic ataxia type 2;C4310716:Developmental and epileptic encephalopathy, 42 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at