ClinVar Miner

Submissions for variant NM_006767.4(LZTR1):c.450C>T (p.Asn150=)

gnomAD frequency: 0.00001  dbSNP: rs560328641
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000586533 SCV000698729 benign not provided 2017-07-10 criteria provided, single submitter clinical testing Variant summary: The LZTR1 c.450C>T (p.Asn150Asn) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may not affect binding of ESE sites. This variant was found in 107/121282 control chromosomes (2 homozygotes) at a frequency of 0.0008822, which is approximately 176 times the estimated maximal expected allele frequency of a pathogenic LZTR1 variant (0.000005), suggesting this variant is likely a benign polymorphism. The variant of interest has not, to our knowledge, been reported in literature. Taken together, this variant is classified as benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV000586533 SCV001717882 benign not provided 2025-01-29 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV001813512 SCV002060546 benign Noonan syndrome and Noonan-related syndrome 2021-01-04 criteria provided, single submitter clinical testing
Ambry Genetics RCV002341503 SCV002640116 benign Hereditary cancer-predisposing syndrome; Cardiovascular phenotype 2020-09-02 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
CeGaT Center for Human Genetics Tuebingen RCV000586533 SCV005893847 likely benign not provided 2024-12-01 criteria provided, single submitter clinical testing LZTR1: BP4, BP7, BS2

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