ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.944C>T (p.Thr315Met)

gnomAD frequency: 0.00033  dbSNP: rs200684272
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000593942 SCV000706232 likely benign not specified 2017-02-20 criteria provided, single submitter clinical testing
Invitae RCV000866112 SCV001007163 benign Nephronophthisis 2023-12-26 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV003409867 SCV004128053 likely benign not provided 2023-01-01 criteria provided, single submitter clinical testing NPHP4: BS2
PreventionGenetics, part of Exact Sciences RCV003945409 SCV004766911 likely benign NPHP4-related condition 2020-01-02 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000593942 SCV001548756 benign not specified no assertion criteria provided clinical testing The NPHP4 p.T315M variant was not identified in the literature but was identified in dbSNP (ID: rs200684272) and ClinVar (classified as benign by Invitae and as likely benign by EGL Genetic Diagnostics). The variant was identified in control databases in 297 of 280526 chromosomes (5 homozygous) at a frequency of 0.001059, and was observed at the highest frequency in the South Asian population in 214 of 30590 chromosomes (5 homozygous) (freq: 0.006996) (Genome Aggregation Database March 6, 2019, v2.1.1). The p.T315 residue is conserved in mammals and computational analyses (MUT Assesor, PolyPhen-2, SIFT, MutationTaster, Revel, FATHMM, MetaLR, DANN) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (Splice AI exome) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.

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