ClinVar Miner

Submissions for variant NM_003126.4(SPTA1):c.6788+11C>T

gnomAD frequency: 0.00002  dbSNP: rs779537034
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
MVZ Dr. Eberhard & Partner Dortmund RCV001290767 SCV001478899 pathogenic Hereditary spherocytosis 2020-03-17 criteria provided, single submitter clinical testing The variant c.6788+11C>T is at low frequency in ensembl and gnomAD (2.1: 4 of 248534 alleles). Multiple lines of computational evidence support a deleterious effect on the gene or gene product. Splice algorithms (SpliceSiteFinder-like, NNSplice, GeneSplicer) recognize a new donor site with higher score than the native donor site. If this new splice donor site would be used 9 nucleotides of the intron will remain within the mRNA and lead to a premature stop codon. Further RNA analysis in our laboratory showed alternatively spliced mRNA with the predicted additional 9 nucleotides from intron 48 and the premature stop codon. Therefore this nonsense mutation is a null variant in a gene where loss of function is a known mechanism of disease and was classified a pathogenic.
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV003234029 SCV003932278 pathogenic Hereditary spherocytosis type 3 2023-01-31 criteria provided, single submitter clinical testing PM2, PM3, PS3_Very Strong

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