16-67174656-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001394979.1(NOL3):c.331G>A(p.Gly111Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000293 in 1,574,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001394979.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOL3 | NM_001394979.1 | c.331G>A | p.Gly111Ser | missense_variant | 3/4 | NP_001381908.1 | ||
NOL3 | NM_001276307.3 | c.331G>A | p.Gly111Ser | missense_variant | 5/6 | NP_001263236.1 | ||
NOL3 | NM_001276309.3 | c.331G>A | p.Gly111Ser | missense_variant | 3/4 | NP_001263238.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000414 AC: 63AN: 152264Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000348 AC: 74AN: 212468Hom.: 0 AF XY: 0.000328 AC XY: 38AN XY: 115864
GnomAD4 exome AF: 0.000280 AC: 398AN: 1422400Hom.: 0 Cov.: 32 AF XY: 0.000301 AC XY: 212AN XY: 704702
GnomAD4 genome AF: 0.000413 AC: 63AN: 152382Hom.: 0 Cov.: 33 AF XY: 0.000376 AC XY: 28AN XY: 74516
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 12, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at