rs61742945
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_018075.5(ANO10):c.627T>C(p.Ala209Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00197 in 1,614,156 control chromosomes in the GnomAD database, including 55 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_018075.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANO10 | NM_018075.5 | c.627T>C | p.Ala209Ala | synonymous_variant | Exon 6 of 13 | ENST00000292246.8 | NP_060545.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0110 AC: 1678AN: 152226Hom.: 28 Cov.: 32
GnomAD3 exomes AF: 0.00274 AC: 680AN: 248368Hom.: 8 AF XY: 0.00199 AC XY: 269AN XY: 134972
GnomAD4 exome AF: 0.00103 AC: 1503AN: 1461812Hom.: 27 Cov.: 32 AF XY: 0.000888 AC XY: 646AN XY: 727212
GnomAD4 genome AF: 0.0111 AC: 1684AN: 152344Hom.: 28 Cov.: 32 AF XY: 0.0101 AC XY: 755AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
not specified Benign:1
- -
Autosomal recessive spinocerebellar ataxia 10 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at