ClinVar Miner

Submissions for variant NM_003126.4(SPTA1):c.3230G>A (p.Arg1077His) (rs199612744)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000999893 SCV000884596 uncertain significance none provided 2020-02-14 criteria provided, single submitter clinical testing
Invitae RCV000756706 SCV001048046 likely benign not provided 2018-05-24 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001101375 SCV001257977 uncertain significance Spherocytosis type 3 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Clinical Services Laboratory,Illumina RCV001101376 SCV001257978 uncertain significance Elliptocytosis 2 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Clinical Services Laboratory,Illumina RCV001101377 SCV001257979 uncertain significance Hereditary pyropoikilocytosis 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Mayo Clinic Laboratories, Mayo Clinic RCV000756706 SCV001713074 uncertain significance not provided 2020-11-06 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000756706 SCV001550745 uncertain significance not provided no assertion criteria provided clinical testing The SPTA1 p.Arg1077His variant was not identified in the literature nor was it identified in LOVD 3.0. The variant was identified in dbSNP (ID: rs199612744), ClinVar (classified as a VUS by ARUP Laboratories) and Cosmic. The variant was also identified in control databases in 214 of 280646 chromosomes (1 homozygous) at a frequency of 0.000763 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 196 of 24178 chromosomes (freq: 0.008107), Latino in 12 of 35342 chromosomes (freq: 0.00034), South Asian in 2 of 30602 chromosomes (freq: 0.000065) and European (non-Finnish) in 4 of 128486 chromosomes (freq: 0.000031), while the variant was not observed in the Ashkenazi Jewish, East Asian, European (Finnish) or Other populations. The p.Arg1077 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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