NM_018075.5:c.1915-5863G>A
Variant names:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_018075.5(ANO10):c.1915-5863G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000888 in 1,535,384 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0046 ( 3 hom., cov: 33)
Exomes 𝑓: 0.00048 ( 4 hom. )
Consequence
ANO10
NM_018075.5 intron
NM_018075.5 intron
Scores
14
Clinical Significance
Conservation
PhyloP100: 1.31
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.004222065).
BP6
Variant 3-43372837-C-T is Benign according to our data. Variant chr3-43372837-C-T is described in ClinVar as [Benign]. Clinvar id is 446832.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0046 (701/152334) while in subpopulation AFR AF= 0.0162 (674/41576). AF 95% confidence interval is 0.0152. There are 3 homozygotes in gnomad4. There are 313 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANO10 | NM_018075.5 | c.1915-5863G>A | intron_variant | Intron 12 of 12 | ENST00000292246.8 | NP_060545.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00457 AC: 695AN: 152216Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.000756 AC: 97AN: 128366Hom.: 1 AF XY: 0.000697 AC XY: 49AN XY: 70300
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GnomAD4 exome AF: 0.000479 AC: 662AN: 1383050Hom.: 4 Cov.: 32 AF XY: 0.000419 AC XY: 286AN XY: 682374
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GnomAD4 genome AF: 0.00460 AC: 701AN: 152334Hom.: 3 Cov.: 33 AF XY: 0.00420 AC XY: 313AN XY: 74486
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
May 21, 2019
Athena Diagnostics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MVP
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at