ClinVar Miner

Submissions for variant NM_212472.2(PRKAR1A):c.770-9G>T (rs562094333)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000464699 SCV000556801 benign Carney complex, type 1 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000781765 SCV000920082 benign not specified 2017-12-15 criteria provided, single submitter clinical testing Variant summary: The PRKAR1A c.770-9G>T variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts the loss of a SC35 binding site. However, these predictions have yet to be confirmed by functional studies. This variant was found in 269/246052 control chromosomes (6 homozygotes)(gnomAD) at a frequency of 0.0010933, which is approximately 583 times the estimated maximal expected allele frequency of a pathogenic PRKAR1A variant (0.0000019), suggesting this variant is likely a benign polymorphism. In addition, one reputable clinical diagnostic laboratory classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
Illumina Clinical Services Laboratory,Illumina RCV001126554 SCV001285766 benign Acrodysostosis 1 with or without hormone resistance 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Illumina Clinical Services Laboratory,Illumina RCV000464699 SCV001288087 benign Carney complex, type 1 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

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