ClinVar Miner

Submissions for variant NM_004371.4(COPA):c.2960+6G>T

gnomAD frequency: 0.00002  dbSNP: rs763329682
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001303437 SCV001492683 uncertain significance Autoimmune interstitial lung disease-arthritis syndrome 2023-06-09 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. ClinVar contains an entry for this variant (Variation ID: 1006401). This variant has not been reported in the literature in individuals affected with COPA-related conditions. This variant is present in population databases (rs763329682, gnomAD 0.02%). This sequence change falls in intron 28 of the COPA gene. It does not directly change the encoded amino acid sequence of the COPA protein. It affects a nucleotide within the consensus splice site.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV001303437 SCV002496076 uncertain significance Autoimmune interstitial lung disease-arthritis syndrome 2022-02-01 criteria provided, single submitter clinical testing COPA NM_004371.3 intron 28 c.2960+6G>T:This variant has not been reported in the literature but is present in 0.01% (2/15276) of Latino alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/1-160292478-C-A?dataset=gnomad_r3). This variant is present in ClinVar (Variation ID:1006401). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant is an intronic variant with no predicted change in the amino acid sequence but may have an unknown effect on splicing. Splice prediction tools do not suggest that this variant may affect splicing. However, further studies are needed to understand its impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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