4-2939339-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001291978.2(NOP14):c.2323G>A(p.Glu775Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000196 in 1,614,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. E775Q) has been classified as Likely benign.
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.2323G>A | p.Glu775Lys | missense_variant | Exon 17 of 18 | ENST00000416614.7 | NP_001278907.1 | |
NOP14 | NM_003703.3 | c.2323G>A | p.Glu775Lys | missense_variant | Exon 17 of 19 | NP_003694.1 | ||
NOP14 | NM_001291979.2 | c.2306+200G>A | intron_variant | Intron 16 of 16 | NP_001278908.1 | |||
NOP14-AS1 | NR_015453.2 | n.2697+547C>T | intron_variant | Intron 2 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000263 AC: 66AN: 251280Hom.: 0 AF XY: 0.000265 AC XY: 36AN XY: 135818
GnomAD4 exome AF: 0.000202 AC: 295AN: 1461724Hom.: 0 Cov.: 31 AF XY: 0.000216 AC XY: 157AN XY: 727134
GnomAD4 genome AF: 0.000144 AC: 22AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2323G>A (p.E775K) alteration is located in exon 17 (coding exon 17) of the NOP14 gene. This alteration results from a G to A substitution at nucleotide position 2323, causing the glutamic acid (E) at amino acid position 775 to be replaced by a lysine (K). 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