Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_000441.2(SLC26A4):c.416-7T>C

Curation Version - 1.0
Curation History
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CA132729

43558 (ClinVar)

Gene: SLC26A4

Condition: Pendred syndrome

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: f4ba1f73-508a-490b-b7d7-7b700fde52f7

Approved on: 2019-10-02

Published on: 2019-10-02

HGVS expressions

NM_000441.2:c.416-7T>C

NM_000441.2(SLC26A4):c.416-7T>C

NM_000441.1:c.416-7T>C

ENST00000265715.7:c.416-7T>C

NC_000007.14:g.107674157T>C

CM000669.2:g.107674157T>C

NC_000007.13:g.107314602T>C

CM000669.1:g.107314602T>C

NC_000007.12:g.107101838T>C

NG_008489.1:g.18523T>C

Benign

BP7 BP4 BA1

PM3

Evidence Links 0

Expert Panel

Hearing Loss VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Hearing Loss VCEP

The filtering allele frequency of the c.416-7T>C variant in SLC29A4 is 0.59% (169/24960) in African chromosomes in gnomAD (BA1). Additionally, computational prediction tools and conservation analysis suggest that the c.416-7T>C variant may not impact the protein (BP4, BP7). In summary, this variant meets criteria to be classified as benign for autosomal recessive Pendred syndrome. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1, BP7, BP4.

BP7

Alamut predict no impact to splicing and the nucleotide is not highly conserved (PhyloP: -0.44).

BP4

No predicted impact to splicing and the nucleotide is not highly conserved.

BA1

The variant is present in 169/24960 in African alleles in gnomAD (0.59% with CI 95%).

PM3

One proband was found with 3 variants in SLC26A4. The other two variants were listed as LB/B in ClinVar and the phase was not confirmed (LMM Internal Data).

Curation History

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