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NM_000441.2(SLC26A4):c.1544+9C>T

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000165255.8
Variation ID:
165255
Description:
single nucleotide variant
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NM_000441.2(SLC26A4):c.1544+9C>T

Allele ID
174162
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q22.3
Genomic location
7: 107696048 (GRCh38) GRCh38 UCSC
7: 107336493 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.107336493C>T
NC_000007.14:g.107696048C>T
NM_000441.2:c.1544+9C>T MANE Select
NG_008489.1:g.40414C>T
Protein change
-
Other names
-
Canonical SPDI
NC_000007.14:107696047:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00220 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00046
The Genome Aggregation Database (gnomAD) 0.00032
Exome Aggregation Consortium (ExAC) 0.00203
1000 Genomes Project 0.00220
Trans-Omics for Precision Medicine (TOPMed) 0.00022
The Genome Aggregation Database (gnomAD), exomes 0.00187
Links
ClinGen: CA177998
dbSNP: rs368970459
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts May 30, 2017 RCV000151900.2
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV000835659.4
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Apr 28, 2017 RCV001164802.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SLC26A4 - - GRCh38
GRCh37
743 819

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(May 30, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000708710.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Feb 24, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000200407.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
1544+9C>T in Intron 13 of SLC26A4: This variant is not expected to have clinical significance because it is not located within the conserved splice consensus … (more)
Likely benign
(Jun 08, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000977460.1
Submitted: (Apr 12, 2019)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Uncertain significance
(Apr 28, 2017)
criteria provided, single submitter
Method: clinical testing
Pendred syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001326952.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(-)
criteria provided, single submitter
Method: research
Pendred syndrome
(Autosomal recessive inheritance)
Allele origin: germline
Broad Institute Rare Disease Group, Broad Institute
Accession: SCV001435186.1
Submitted: (Mar 10, 2020)
Evidence details
Publications
PubMed (3)
Comment:
The heterozygous c.1544+9C>T variant in SLC26A4 has been identified in 3 individuals with Pendred syndrome (PMID: 21704276, 25214170, 21961810), but has also been identified in … (more)
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001055904.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jun 14, 2020)
no assertion criteria provided
Method: clinical testing
Pendred syndrome
Allele origin: germline
Natera, Inc.
Accession: SCV001459873.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Intronic variants of SLC26A4 gene enhance splicing efficiency in hybrid minigene assay. Kallel-Bouattour R Gene 2017 PMID: 28389359
Identification and genotype/phenotype correlation of mutations in a large German cohort with hearing loss. Beck C European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery 2015 PMID: 25214170
Extremely discrepant mutation spectrum of SLC26A4 between Chinese patients with isolated Mondini deformity and enlarged vestibular aqueduct. Huang S Journal of translational medicine 2011 PMID: 21961810
Mutation analysis of SLC26A4 for Pendred syndrome and nonsyndromic hearing loss by high-resolution melting. Chen N The Journal of molecular diagnostics : JMD 2011 PMID: 21704276
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SLC26A4 - - - -

Text-mined citations for rs368970459...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 27, 2021