ClinVar Miner

Submissions for variant NM_003924.4(PHOX2B):c.870C>A (p.Pro290=) (rs17885864)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000151647 SCV000199899 benign not specified 2014-10-02 criteria provided, single submitter clinical testing p.Pro290Pro in exon 3 of PHOX2B: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and has been identi fied in 5.6% (246/4406) of African American chromosomes by the NHLBI Exome Seque ncing Project (http://evs.gs.washington.edu/EVS/; dbSNP rs17885864).
PreventionGenetics,PreventionGenetics RCV000151647 SCV000309893 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000303623 SCV000449530 benign Neuroblastoma 2 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
Illumina Clinical Services Laboratory,Illumina RCV000358376 SCV000449531 benign Congenital central hypoventilation 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.
GeneDx RCV000151647 SCV000518956 benign not specified 2016-07-25 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.
Invitae RCV000358376 SCV000557091 benign Congenital central hypoventilation 2019-12-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000151647 SCV000604626 benign not specified 2019-03-28 criteria provided, single submitter clinical testing
Ambry Genetics RCV000562765 SCV000664960 benign Hereditary cancer-predisposing syndrome 2016-11-23 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Integrated Genetics/Laboratory Corporation of America RCV000589447 SCV000698221 benign not provided 2016-05-17 criteria provided, single submitter clinical testing Variant summary: The PHOX2B c.870C>A (p.Pro290Pro) variant causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools calculating no significant effect on splicing, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 2837/114102 (52 homozygotes, 1/40, frequency: 0.0248637), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic PHOX2B variant of 1/1250000 (frequenc: 0.0000008), suggesting this variant is likely a benign polymorphism. In addition, a reputable clinical laboratory cites the variant as "benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000151647 SCV000706083 benign not specified 2017-02-02 criteria provided, single submitter clinical testing

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