rs34104729
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001346468.2(ANO10):c.-12+3041T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0295 in 152,276 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.030 ( 86 hom., cov: 32)
Consequence
ANO10
NM_001346468.2 intron
NM_001346468.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.340
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0295 (4494/152276) while in subpopulation NFE AF= 0.0393 (2673/68004). AF 95% confidence interval is 0.0381. There are 86 homozygotes in gnomad4. There are 2173 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 86 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANO10 | NM_001346468.2 | c.-12+3041T>C | intron_variant | ||||
ANO10 | NM_001346469.2 | c.-12+3041T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANO10 | ENST00000413397.5 | c.-12+3041T>C | intron_variant | 4 | |||||
ANO10 | ENST00000428831.1 | c.-106+2139T>C | intron_variant | 5 | |||||
ANO10 | ENST00000436073.1 | c.-103+2065T>C | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0295 AC: 4496AN: 152158Hom.: 86 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 genome ? AF: 0.0295 AC: 4494AN: 152276Hom.: 86 Cov.: 32 AF XY: 0.0292 AC XY: 2173AN XY: 74470
GnomAD4 genome
?
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4494
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32
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2173
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74470
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38
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at