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

  • See Evidence submitted by expert panel for details.

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

CA132729

43558 (ClinVar)

Gene: SLC26A4
Condition: Pendred syndrome
Inheritance Mode: Autosomal recessive inheritance
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
More

Benign

Met criteria codes 3
BA1 BP4 BP7
Not Met criteria codes 1
PM3

Evidence Links 0

Expert Panel

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.
Met criteria codes
BA1
The variant is present in 169/24960 in African alleles in gnomAD (0.59% with CI 95%).
BP4
No predicted impact to splicing and the nucleotide is not highly conserved.
BP7
Alamut predict no impact to splicing and the nucleotide is not highly conserved (PhyloP: -0.44).
Not Met criteria codes
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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