chr3-43366831-A-AC
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BS1_Supporting
The NM_018075.5(ANO10):c.*74_*75insG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,438,650 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00017 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
ANO10
NM_018075.5 3_prime_UTR
NM_018075.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.104
Genes affected
ANO10 (HGNC:25519): (anoctamin 10) The transmembrane protein encoded by this gene belongs to the anoctamin family of calcium-activated chloride channels, also known as the transmembrane 16 family. The encoded protein contains eight transmembrane domains with cytosolic N- and C-termini. Defects in this gene may cause autosomal recessive spinocerebellar ataxia-10. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000172 (26/151600) while in subpopulation EAS AF= 0.00291 (15/5146). AF 95% confidence interval is 0.0018. There are 0 homozygotes in gnomad4. There are 13 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANO10 | NM_018075.5 | c.*74_*75insG | 3_prime_UTR_variant | 13/13 | ENST00000292246.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANO10 | ENST00000292246.8 | c.*74_*75insG | 3_prime_UTR_variant | 13/13 | 1 | NM_018075.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000172 AC: 26AN: 151488Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000146 AC: 188AN: 1287050Hom.: 0 Cov.: 21 AF XY: 0.000147 AC XY: 94AN XY: 640468
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GnomAD4 genome AF: 0.000172 AC: 26AN: 151600Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74106
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal recessive cerebellar ataxia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at