4-2938913-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001291978.2(NOP14):c.2492G>A(p.Arg831Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000052 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R831W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001291978.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOP14 | NM_001291978.2 | c.2492G>A | p.Arg831Gln | missense_variant | Exon 18 of 18 | ENST00000416614.7 | NP_001278907.1 | |
NOP14 | NM_003703.3 | c.2492G>A | p.Arg831Gln | missense_variant | Exon 18 of 19 | NP_003694.1 | ||
NOP14 | NM_001291979.2 | c.2307-586G>A | intron_variant | Intron 16 of 16 | NP_001278908.1 | |||
NOP14-AS1 | NR_015453.2 | n.2697+121C>T | intron_variant | Intron 2 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251424Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135902
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461766Hom.: 0 Cov.: 31 AF XY: 0.0000660 AC XY: 48AN XY: 727174
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2492G>A (p.R831Q) alteration is located in exon 18 (coding exon 18) of the NOP14 gene. This alteration results from a G to A substitution at nucleotide position 2492, causing the arginine (R) at amino acid position 831 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at