ClinVar Miner

Submissions for variant NM_018706.7(DHTKD1):c.2659-3_2659-2del

dbSNP: rs761529786
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001810805 SCV002048401 uncertain significance not provided 2021-11-19 criteria provided, single submitter clinical testing The DHTKD1 c.2659-3_2659-2delTA variant, to our knowledge, is not reported in the medical literature or gene specific databases. The variant is reported in the African population with an allele frequency of 0.1% (25/24,968 alleles) in the Genome Aggregation Database. This variant disrupts the canonical splice acceptor site of intron 16, which is likely to negatively impact gene function. Due to limited information, the clinical significance of the c.2659-3_2659-2delTA variant is uncertain at this time.
Labcorp Genetics (formerly Invitae), Labcorp RCV002074154 SCV002422357 likely benign 2-aminoadipic 2-oxoadipic aciduria 2023-10-29 criteria provided, single submitter clinical testing
Ambry Genetics RCV002542332 SCV003555741 uncertain significance Inborn genetic diseases 2021-08-18 criteria provided, single submitter clinical testing The c.2659-3_2659-2delTA alteration is located in intron 16 of the DHTKD1 gene. This alteration consists of a deletion of 2 nucleotides at nucleotide position c.2659-3. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003226492 SCV003923132 uncertain significance not specified 2023-03-27 criteria provided, single submitter clinical testing Variant summary: DHTKD1 c.2659-3_2659-2delTA alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. The variant allele was found at a frequency of 9.9e-05 in 251458 control chromosomes (gnomAD). To our knowledge, no occurrence of c.2659-3_2659-2delTA in individuals affected with 2-Aminoadipic 2-Oxoadipic Aciduria and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as VUS (n=2) and likely benign (n=1). Based on the evidence outlined above, the variant was classified as uncertain significance.

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