ClinVar Miner

Submissions for variant NM_002878.4(RAD51D):c.481-7G>A

gnomAD frequency: 0.00169  dbSNP: rs145832514
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000179411 SCV000171273 benign not specified 2014-04-01 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Eurofins NTD LLC (GA) RCV000179411 SCV000231657 likely benign not specified 2015-01-07 criteria provided, single submitter clinical testing
Invitae RCV000204059 SCV000262322 benign Breast-ovarian cancer, familial, susceptibility to, 4 2020-12-08 criteria provided, single submitter clinical testing
Counsyl RCV000204059 SCV000488984 likely benign Breast-ovarian cancer, familial, susceptibility to, 4 2016-07-29 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000179411 SCV000602159 likely benign not specified 2017-02-14 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000580868 SCV000686460 likely benign Hereditary cancer-predisposing syndrome 2015-09-21 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000587972 SCV000698106 benign not provided 2016-02-15 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000587972 SCV000889824 benign not provided 2018-06-20 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000179411 SCV002071944 likely benign not specified 2019-04-25 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000580868 SCV002534822 benign Hereditary cancer-predisposing syndrome 2020-10-23 criteria provided, single submitter curation
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001358081 SCV001553729 likely benign Malignant tumor of breast no assertion criteria provided clinical testing The RAD51D c.481-7G>A variant was identified in 2 of 6082 proband chromosomes (frequency: 0.0003) from individuals or families with breast cancer or Lynch syndrome (Tung 2015, Yurgelun 2015). The variant was also identified in dbSNP (ID: rs145832514 as "With other allele") and ClinVar (3x as benign by GeneDx, Invitae, and Integrated Genetics/Laboratory Corporation of America and 4x as likely benign by Counsyl, Color Genomics, EGL Genetic Diagnostics, and Quest Diagnostics Nichols Institute). The variant was not identified in Cosmic. The variant was identified in control databases in 134 of 268084 chromosomes at a frequency of 0.0005, increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 124 of 22892 chromosomes (freq: 0.005), Other in 1 of 6294 chromosomes (freq: 0.0002), Latino in 6 of 33736 chromosomes (freq: 0.0002), European in 1 of 121706 chromosomes (freq: 0.000008), East Asian in 1 of 18750 chromosomes (freq: 0.00005), and South Asian in 1 of 29640 chromosomes (freq: 0.00003), while the variant was not observed in the Ashkenazi Jewish or Finnish populations. The c.481-7G>A variant is located in the 3' splice region but does not affect the invariant -1 and -2 positions. However, positions -3 and -5 to -12 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. However, 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing; however, this information is not predictive enough to rule out pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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