rs117748217
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_031418.4(ANO3):c.2811C>T(p.Asp937=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00945 in 1,613,220 control chromosomes in the GnomAD database, including 122 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0075 ( 11 hom., cov: 32)
Exomes 𝑓: 0.0096 ( 111 hom. )
Consequence
ANO3
NM_031418.4 synonymous
NM_031418.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.861
Genes affected
ANO3 (HGNC:14004): (anoctamin 3) The protein encoded by this gene belongs to the TMEM16 family of predicted membrane proteins, that are also known as anoctamins. While little is known about the function of this gene, mutations in this gene have been associated with some cases of autosomal dominant craniocervical dystonia. Cells from individuals with a mutation in this gene exhibited abnormalities in endoplasmic reticulum-dependent calcium signaling. Studies in rat show that the rat ortholog of this protein interacts with, and modulates the activity of a sodium-activated potassium channel. Deletion of this gene caused increased pain sensitivity in the rat model system. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.27).
BP6
?
Variant 11-26660309-C-T is Benign according to our data. Variant chr11-26660309-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 412868.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-26660309-C-T is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=0.861 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00754 (1148/152220) while in subpopulation AMR AF= 0.014 (214/15260). AF 95% confidence interval is 0.0125. There are 11 homozygotes in gnomad4. There are 525 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1148 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANO3 | NM_031418.4 | c.2811C>T | p.Asp937= | synonymous_variant | 27/27 | ENST00000256737.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANO3 | ENST00000256737.8 | c.2811C>T | p.Asp937= | synonymous_variant | 27/27 | 1 | NM_031418.4 | P3 | |
ANO3 | ENST00000672621.1 | c.2994C>T | p.Asp998= | synonymous_variant | 28/28 | ||||
ANO3 | ENST00000525139.5 | c.2763C>T | p.Asp921= | synonymous_variant | 27/27 | 5 | |||
ANO3 | ENST00000531568.1 | c.2373C>T | p.Asp791= | synonymous_variant | 24/24 | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00754 AC: 1147AN: 152102Hom.: 11 Cov.: 32
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GnomAD3 exomes AF: 0.00873 AC: 2189AN: 250776Hom.: 21 AF XY: 0.00913 AC XY: 1238AN XY: 135552
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GnomAD4 exome AF: 0.00965 AC: 14097AN: 1461000Hom.: 111 Cov.: 31 AF XY: 0.00966 AC XY: 7020AN XY: 726792
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GnomAD4 genome ? AF: 0.00754 AC: 1148AN: 152220Hom.: 11 Cov.: 32 AF XY: 0.00705 AC XY: 525AN XY: 74416
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | ANO3: BP4, BP7, BS1, BS2 - |
Dystonia 24 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Dystonic disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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