3-196659822-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_198565.3(NRROS):c.179G>A(p.Arg60Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000669 in 1,613,944 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_198565.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000585 AC: 89AN: 152072Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000410 AC: 103AN: 250982Hom.: 0 AF XY: 0.000435 AC XY: 59AN XY: 135732
GnomAD4 exome AF: 0.000678 AC: 991AN: 1461754Hom.: 0 Cov.: 30 AF XY: 0.000634 AC XY: 461AN XY: 727184
GnomAD4 genome AF: 0.000585 AC: 89AN: 152190Hom.: 0 Cov.: 31 AF XY: 0.000578 AC XY: 43AN XY: 74398
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 60 of the NRROS protein (p.Arg60Gln). This variant is present in population databases (rs140967612, gnomAD 0.07%). This variant has not been reported in the literature in individuals affected with NRROS-related conditions. ClinVar contains an entry for this variant (Variation ID: 1367446). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt NRROS protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Seizures, early-onset, with neurodegeneration and brain calcifications Uncertain:1
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Inborn genetic diseases Benign:1
This alteration is classified as likely 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at