ClinVar Miner

Submissions for variant NM_000135.4(FANCA):c.79+10C>T

gnomAD frequency: 0.00015  dbSNP: rs573174362
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001343713 SCV001537716 uncertain significance Fanconi anemia 2022-02-09 criteria provided, single submitter clinical testing This sequence change falls in intron 1 of the FANCA gene. It does not directly change the encoded amino acid sequence of the FANCA protein. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with FANCA-related conditions. ClinVar contains an entry for this variant (Variation ID: 1040126). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV003478788 SCV004218643 uncertain significance not provided 2023-07-07 criteria provided, single submitter clinical testing To the best of our knowledge, this variant has not been reported in the published literature. The frequency of this variant in the general population, 0.00048 (4/8398 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant does not affect FANCA mRNA splicing . Based on the available information, we are unable to determine the clinical significance of this variant.
Natera, Inc. RCV001343713 SCV002093148 uncertain significance Fanconi anemia 2020-03-04 no assertion criteria provided clinical testing
Genetic Services Laboratory, University of Chicago RCV003151303 SCV003839505 uncertain significance not specified 2022-11-02 no assertion criteria provided clinical testing DNA sequence analysis of the FANCA gene demonstrated a sequence change in intron 1, c.79+10C>T. This change does not appear to have been previously described in individuals with FANCA-related disorders. This sequence change has been described in the gnomAD database with a frequency of 0.01% in the Latino subpopulation (dbSNP rs573174362). This sequence change is not predicted to have a deleterious effect on splicing based on in-silico splice prediction programs. It is possible that this sequence change represents a benign sequence change in the FANCA gene that has not been identified to date. The functional significance of this sequence change is not known at present and its contribution to this individual's disease phenotype cannot definitively be determined.

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