ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.2363+10dup

gnomAD frequency: 0.00058  dbSNP: rs760632806
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000341107 SCV000355787 uncertain significance Chédiak-Higashi syndrome 2016-06-14 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000341107 SCV000743804 likely benign Chédiak-Higashi syndrome 2017-11-01 criteria provided, single submitter clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000341107 SCV000745220 likely benign Chédiak-Higashi syndrome 2017-06-28 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000341107 SCV001596998 likely benign Chédiak-Higashi syndrome 2024-01-31 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001699343 SCV004039505 likely benign not specified 2023-08-15 criteria provided, single submitter clinical testing Variant summary: LYST c.2363+10dupT alters a nucleotide located at a position not widely known to affect splicing. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00059 in 281428 control chromosomes, predominantly at a frequency of 0.0011 within the Latino subpopulation in the gnomAD database. This frequency is equal to estimated for a pathogenic variant in LYST causing Chediak-Higashi Syndrome (0.0011 vs 0.0011), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Latino origin. To our knowledge, no occurrence of c.2363+10dupT in individuals affected with Chediak-Higashi Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Four submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 classified this variant as uncertain significance (n=1) and likely benign (n=3). Based on the evidence outlined above, the variant was classified as likely benign.
Clinical Genetics, Academic Medical Center RCV001699343 SCV001926050 benign not specified no assertion criteria provided clinical testing

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