chr19-45940594-A-AGGC
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_002516.4(NOVA2):c.747_748insGCC(p.Ala249dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000492 in 1,423,038 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 34)
Exomes 𝑓: 0.0000047 ( 0 hom. )
Consequence
NOVA2
NM_002516.4 inframe_insertion
NM_002516.4 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.26
Genes affected
NOVA2 (HGNC:7887): (NOVA alternative splicing regulator 2) Enables sequence-specific mRNA binding activity. Involved in neuron differentiation and regulation of alternative mRNA splicing, via spliceosome. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOVA2 | NM_002516.4 | c.747_748insGCC | p.Ala249dup | inframe_insertion | 4/4 | ENST00000263257.6 | |
NOVA2 | XM_006723230.4 | c.420_421insGCC | p.Ala140dup | inframe_insertion | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOVA2 | ENST00000263257.6 | c.747_748insGCC | p.Ala249dup | inframe_insertion | 4/4 | 1 | NM_002516.4 | P1 | |
NOVA2 | ENST00000676183.1 | c.939_940insGCC | p.Ala313dup | inframe_insertion | 4/4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000663 AC: 1AN: 150902Hom.: 0 Cov.: 34
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GnomAD4 exome AF: 0.00000472 AC: 6AN: 1272136Hom.: 0 Cov.: 61 AF XY: 0.00000479 AC XY: 3AN XY: 626294
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2023 | This variant, c.745_747dup, results in the insertion of 1 amino acid(s) of the NOVA2 protein (p.Ala249dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with NOVA2-related conditions. 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. - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at