ClinVar Miner

Submissions for variant NM_001206999.2(CIT):c.1296-5C>T

gnomAD frequency: 0.00202  dbSNP: rs182092782
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000905117 SCV001049682 benign not provided 2024-12-02 criteria provided, single submitter clinical testing
GeneDx RCV000905117 SCV001758108 likely benign not provided 2021-01-27 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV001818780 SCV002068304 likely benign not specified 2018-01-19 criteria provided, single submitter clinical testing
Ambry Genetics RCV002537581 SCV003551308 uncertain significance Inborn genetic diseases 2020-12-19 criteria provided, single submitter clinical testing The c.1296-5C>T intronic alteration consists of a C to T substitution 5 nucleotides before coding exon 10 in the CIT gene. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001818780 SCV005884434 benign not specified 2024-12-26 criteria provided, single submitter clinical testing Variant summary: CIT c.1296-5C>T alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00038 in 250332 control chromosomes, predominantly at a frequency of 0.0054 within the African or African-American subpopulation in the gnomAD database. The observed variant frequency within African or African-American control individuals in the gnomAD database exceeds the estimated maximal expected allele frequency for a pathogenic variant in CIT causing Microcephaly 17, Primary, Autosomal Recessive phenotype. To our knowledge, no occurrence of c.1296-5C>T in individuals affected with Microcephaly 17, Primary, Autosomal Recessive and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 730328). Based on the evidence outlined above, the variant was classified as benign.

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