ClinVar Miner

Submissions for variant NM_000038.6(APC):c.4614_4619del (p.Ser1539_Glu1540del)

dbSNP: rs767417584
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV000581120 SCV000681677 uncertain significance Hereditary cancer-predisposing syndrome 2020-03-13 criteria provided, single submitter clinical testing This variant causes an in-frame deletion of 2 amino acids at exon 15 of the of the APC protein. Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has been identified in 1/250238 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Ambry Genetics RCV000581120 SCV001184558 uncertain significance Hereditary cancer-predisposing syndrome 2021-05-06 criteria provided, single submitter clinical testing The c.4614_4619delATCAGA variant (also known as p.S1539_E1540del) is located in coding exon 15 of the APC gene. This variant results from an in-frame ATCAGA deletion at nucleotide positions 4614 to 4619. This results in the in-frame deletion of a at codon 1539. This amino acid region is not well conserved in available vertebrate species. In addition, this alteration is predicted to be neutral by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Invitae RCV003653181 SCV001389135 uncertain significance Familial adenomatous polyposis 1 2023-10-13 criteria provided, single submitter clinical testing This variant, c.4614_4619del, results in the deletion of 2 amino acid(s) of the APC protein (p.Ser1539_Glu1540del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs767417584, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with APC-related conditions. ClinVar contains an entry for this variant (Variation ID: 489455). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

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