ClinVar Miner

Submissions for variant NM_015120.4(ALMS1):c.39_77= (p.Glu13_Glu26=) (rs55889738)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000173443 SCV000224558 likely benign not specified 2014-08-21 criteria provided, single submitter clinical testing
Invitae RCV001079667 SCV000261994 benign Alstrom syndrome 2019-12-31 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000224308 SCV000280788 likely benign not provided 2016-03-18 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia RCV000173443 SCV000297249 benign not specified 2015-09-03 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000173443 SCV000312405 benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000173443 SCV000569352 likely benign not specified 2017-03-30 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.
Integrated Genetics/Laboratory Corporation of America RCV000173443 SCV000864082 benign not specified 2018-03-12 criteria provided, single submitter clinical testing Variant summary: ALMS1 c.72_74delGGA (p.Glu29del, alternative name c.75_77delGGA) results in an in-frame deletion that is predicted to remove one amino acid from the repetitive region of the encoded protein. The variant allele was found at a frequency of 0.058 in 118306 control chromosomes in the gnomAD database, including 292 homozygotes. The observed variant frequency is approximately 26.064 fold of the estimated maximal expected allele frequency for a pathogenic variant in ALMS1 causing Cardiomyopathy phenotype (0.0022), strongly suggesting that the variant is benign. c.72_74delGGA has been reported in the literature in affected individuals with comparible frequency as in controls. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.

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