ClinVar Miner

Submissions for variant NM_000369.5(TSHR):c.1377G>A (p.Ala459=)

dbSNP: rs113951800
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000243995 SCV000303879 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000346528 SCV000389146 benign Familial hyperthyroidism due to mutations in TSH receptor 2018-01-13 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 Laboratory Services, Illumina RCV000384951 SCV000389147 likely benign Hypothyroidism due to TSH receptor mutations 2018-01-13 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
GeneDx RCV001574623 SCV001801476 likely benign not provided 2019-03-19 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001574623 SCV004508406 benign not provided 2024-01-31 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV001574623 SCV005217815 likely benign not provided criteria provided, single submitter not provided
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000243995 SCV001551772 benign not specified no assertion criteria provided clinical testing The TSHR p.Ala459Ala variant was identified in 5 of 194 proband chromosomes (frequency: 0.0258) from individuals with primary congenital hypothyroidism or autonomously functioning thyroid nodules (Alves_2010_PMID:21714466; Gabriel_1999_PMID:10487707). In a case study, the TSHR gene was sequenced in a girl with severe non-autoimmune hyperthyroidism and her mother with autoimmune thyroid disease; the mother was found to carry the p.A459A variant but it was not present in the girl (Scaglia_2012_PMID:23295291). The variant was identified in dbSNP (ID: rs113951800), ClinVar (classified as likely benign by Illumina and as benign by PreventionGenetics) and LOVD 3.0 (classified as benign) but was not identified in Cosmic. The variant was identified in control databases in 4983 of 282856 chromosomes (63 homozygous) at a frequency of 0.017617 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: South Asian in 1259 of 30616 chromosomes (freq: 0.04112), European (non-Finnish) in 2690 of 129178 chromosomes (freq: 0.02082), Ashkenazi Jewish in 184 of 10370 chromosomes (freq: 0.01774), Other in 126 of 7224 chromosomes (freq: 0.01744), European (Finnish) in 344 of 25112 chromosomes (freq: 0.0137), Latino in 256 of 35440 chromosomes (freq: 0.007223), African in 108 of 24966 chromosomes (freq: 0.004326), and East Asian in 16 of 19950 chromosomes (freq: 0.000802). The p.Ala459Ala variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. However, four of four in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing and the creation of a new 3' splice site. However, this has not been confirmed through RNA analysis and is not predictive enough to assume pathogenicity. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.

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