Submissions for variant NM_014956.5(CEP164):c.347dup (p.Glu117fs)

Total submissions: 3

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Neuberg Centre For Genomic Medicine, NCGM	RCV003338094	SCV004047007	likely pathogenic	Nephronophthisis 15		criteria provided, single submitter	clinical testing	The frame shift (p.Glu117GlyfsTer88) variant has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Glu117GlyfsTer88 variant is novel (not in any individuals) in 1000 Genomes and has allele frequency of 2.18% in gnomAD database. This variant has not been reported to the ClinVar database. This variant causes a frameshift starting with codon Glutamic Acid 117, changes this amino acid to Glycine residue, and creates a premature Stop codon at position 88 of the new reading frame, denoted p.Glu117GlyfsTer88. For these reasons, this variant has been classified as Likely Pathogenic. In the absence of another reportable variant the molecular diagnosis is not confirmed.
Labcorp Genetics (formerly Invitae), Labcorp	RCV003338094	SCV004661320	benign	Nephronophthisis 15	2023-11-24	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV004753675	SCV005354957	uncertain significance	CEP164-related disorder	2024-09-11	no assertion criteria provided	clinical testing	The CEP164 c.347dupA variant is predicted to result in a frameshift and premature protein termination (p.Glu117Glyfs*88). To our knowledge, this variant has not been reported in the literature. This variant is reported in 3.1% of alleles in individuals of South Asian descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.