X-71290709-C-CCAG
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_007363.5(NONO):c.81_83dupGCA(p.Gln27dup) variant causes a disruptive inframe insertion change. The variant allele was found at a frequency of 0.0000128 in 1,090,952 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007363.5 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NONO | NM_007363.5 | c.81_83dupGCA | p.Gln27dup | disruptive_inframe_insertion | Exon 3 of 12 | ENST00000276079.13 | NP_031389.3 | |
NONO | NM_001145408.2 | c.81_83dupGCA | p.Gln27dup | disruptive_inframe_insertion | Exon 4 of 13 | NP_001138880.1 | ||
NONO | NM_001145409.2 | c.81_83dupGCA | p.Gln27dup | disruptive_inframe_insertion | Exon 2 of 11 | NP_001138881.1 | ||
NONO | NM_001145410.2 | c.-113-1061_-113-1059dupGCA | intron_variant | Intron 1 of 9 | NP_001138882.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.00000591 AC: 1AN: 169159Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 56627
GnomAD4 exome AF: 0.0000128 AC: 14AN: 1090952Hom.: 0 Cov.: 29 AF XY: 0.0000168 AC XY: 6AN XY: 356932
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not provided Uncertain:1
Not observed at significant frequency in large population cohorts (gnomAD); In-frame insertion of 1 amino acid in a non-repeat region; In silico analysis supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at