ClinVar Miner

Submissions for variant NM_001083962.2(TCF4):c.269A>G (p.Asn90Ser)

gnomAD frequency: 0.00067  dbSNP: rs143244149
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel RCV000332791 SCV001711968 benign Pitt-Hopkins syndrome 2021-03-26 reviewed by expert panel curation The allele frequency of the p.Asn90Ser variant in TCF4 is 1.5% in Ashkenazi Jewish sub population in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). The p.Asn90Ser variant is observed in at least 2 unaffected individuals (internal database) (BS2). Computational analysis prediction tools suggest that the p.Asn90Ser variant does not have a deleterious impact; however this information does not predict clinical significance on its own (BP4). In summary, the p.Asn90Ser variant in TCF4 is classified as benign based on the ACMG/AMP criteria (BA1, BS2, BP4).
Eurofins Ntd Llc (ga) RCV000154003 SCV000203628 likely benign not specified 2015-06-25 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000332791 SCV000409536 benign Pitt-Hopkins syndrome 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.
Invitae RCV000332791 SCV000646126 benign Pitt-Hopkins syndrome 2024-01-22 criteria provided, single submitter clinical testing
GeneDx RCV000154003 SCV000730146 benign not specified 2017-05-12 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Ambry Genetics RCV002316975 SCV000850494 benign Inborn genetic diseases 2017-03-21 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.
Genetic Services Laboratory, University of Chicago RCV000154003 SCV002067475 benign not specified 2017-12-13 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV003884365 SCV004700530 likely benign not provided 2024-01-01 criteria provided, single submitter clinical testing TCF4: BS1

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