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.1708-18T>A

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Curation History
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CA4432923

256155 (ClinVar)

Gene: SLC26A4

Condition: Pendred syndrome

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: 9aa2ed65-e713-4357-b0b9-2fbfe5898a07

Approved on: 2020-03-18

Published on: 2020-03-19

HGVS expressions

NM_000441.2:c.1708-18T>A

NM_000441.2(SLC26A4):c.1708-18T>A

NC_000007.14:g.107701083T>A

CM000669.2:g.107701083T>A

NC_000007.13:g.107341528T>A

CM000669.1:g.107341528T>A

NC_000007.12:g.107128764T>A

NG_008489.1:g.45449T>A

NM_000441.1:c.1708-18T>A

ENST00000265715.7:c.1708-18T>A

ENST00000480841.5:n.557-18T>A

ENST00000492030.2:n.91-744T>A

Benign

BA1 BP4 BP7

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 (the lower threshold of the 95% CI of 1456/25104) of the c.1708-18T>A variant in the SLC26A4 gene is 5.55% for European (Finnish) chromosomes by gnomAD v2.1.1, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1). This silent variant in SLC26A4 is not predicted by the computational prediction analysis using MaxEntScan to impact splicing (BP7, BP4). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1, BP7, BP4.

BA1

The variant is present in 5.55% (1456/25104) (95% CI) of European (Finnish) chromosomes in gnomAD v2.1.1 and in 5.35% (599/10464) (95% CI) of European (Finnish) chromosomes in gnomAD v3.

BP4

No splicing impact indicated by Alamut, squirrel and manatee have different nucleotides at this position.

BP7

No splicing effects indicated by predictors in Alamut including MaxEntScan.

Curation History

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