chr19-13207408-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP2BP4BP6_Very_StrongBS2
The NM_001127222.2(CACNA1A):c.7426T>C(p.Tyr2476His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000213 in 1,534,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. Y2476Y) has been classified as Benign.
Frequency
Consequence
NM_001127222.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1A | NM_001127222.2 | c.7426T>C | p.Tyr2476His | missense_variant | 47/47 | ENST00000360228.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1A | ENST00000360228.11 | c.7426T>C | p.Tyr2476His | missense_variant | 47/47 | 1 | NM_001127222.2 |
Frequencies
GnomAD3 genomes ? AF: 0.000126 AC: 19AN: 151160Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000796 AC: 11AN: 138216Hom.: 0 AF XY: 0.000105 AC XY: 8AN XY: 76536
GnomAD4 exome AF: 0.000223 AC: 308AN: 1382922Hom.: 0 Cov.: 30 AF XY: 0.000212 AC XY: 145AN XY: 684238
GnomAD4 genome ? AF: 0.000126 AC: 19AN: 151160Hom.: 0 Cov.: 31 AF XY: 0.000122 AC XY: 9AN XY: 73826
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 09, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 29, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at