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NM_018075.5(ANO10):c.337+1G>A AND not provided

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Dec 19, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003221843.11

Allele description [Variation Report for NM_018075.5(ANO10):c.337+1G>A]

NM_018075.5(ANO10):c.337+1G>A

Gene:
ANO10:anoctamin 10 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.33
Genomic location:
Preferred name:
NM_018075.5(ANO10):c.337+1G>A
HGVS:
  • NC_000003.12:g.43600383C>T
  • NG_028216.2:g.96212G>A
  • NM_001204831.3:c.337+1G>A
  • NM_001204832.3:c.140-1717G>A
  • NM_001204833.3:c.139+5331G>A
  • NM_001204834.3:c.337+1G>A
  • NM_001346463.2:c.337+1G>A
  • NM_001346464.2:c.337+1G>A
  • NM_001346465.2:c.337+1G>A
  • NM_001346466.2:c.140-1717G>A
  • NM_001346467.2:c.337+1G>A
  • NM_001346468.2:c.337+1G>A
  • NM_001346469.2:c.140-1717G>A
  • NM_018075.5:c.337+1G>AMANE SELECT
  • NC_000003.11:g.43641875C>T
  • NM_018075.3:c.337+1G>A
Links:
dbSNP: rs765592794
NCBI 1000 Genomes Browser:
rs765592794
Molecular consequence:
  • NM_001204832.3:c.140-1717G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001204833.3:c.139+5331G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001346466.2:c.140-1717G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001346469.2:c.140-1717G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001204831.3:c.337+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001204834.3:c.337+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001346463.2:c.337+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001346464.2:c.337+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001346465.2:c.337+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001346467.2:c.337+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001346468.2:c.337+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_018075.5:c.337+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003916808CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Pathogenic
(Mar 1, 2023)
germlineclinical testing

Citation Link,

SCV004509263Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Dec 19, 2023)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Autosomal recessive cerebellar ataxia type 3 due to ANO10 mutations: delineation and genotype-phenotype correlation study.

Renaud M, Anheim M, Kamsteeg EJ, Mallaret M, Mochel F, Vermeer S, Drouot N, Pouget J, Redin C, Salort-Campana E, Kremer HP, Verschuuren-Bemelmans CC, Muller J, Scheffer H, Durr A, Tranchant C, Koenig M.

JAMA Neurol. 2014 Oct;71(10):1305-10. doi: 10.1001/jamaneurol.2014.193.

PubMed [citation]
PMID:
25089919
See all PubMed Citations (4)

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV003916808.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

ANO10: PVS1, PM2

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Invitae, SCV004509263.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change affects a donor splice site in intron 3 of the ANO10 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ANO10 are known to be pathogenic (PMID: 25089919). This variant is present in population databases (rs765592794, gnomAD 0.008%). Disruption of this splice site has been observed in individual(s) with spinocerebellar ataxia (PMID: 30515630). ClinVar contains an entry for this variant (Variation ID: 210186). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 15, 2024