ClinVar Miner

Submissions for variant NM_020800.3(IFT80):c.1678A>G (p.Asn560Asp)

gnomAD frequency: 0.00011  dbSNP: rs202145480
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001001024 SCV000441905 uncertain significance Asphyxiating thoracic dystrophy 2 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Invitae RCV000336393 SCV000544761 likely benign Jeune thoracic dystrophy 2023-10-29 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001001024 SCV001158132 uncertain significance Asphyxiating thoracic dystrophy 2 2019-02-06 criteria provided, single submitter clinical testing The IFT80 c.1678A>G; p.Asn560Asp variant (rs202145480), to our knowledge, has not been described in the medical literature but is listed as a variant of unknown significance in ClinVar (Variation ID: 343967). It is observed at an overall frequency of 0.016% (46/282116 alleles) with increased frequency in the Ashkenazi Jewish population (0.35%) in the Genome Aggregation Database. The asparagine at codon 560 is moderately conserved, and computational algorithms (PolyPhen-2, SIFT) predict that this variant is tolerated. However, due to the lack of clinical and functional data regarding this variant, its clinical significance cannot be determined with certainty.

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