19-45940207-CGCCCCCTCCGCCCGCCCCGCCGCCCGCCCCG-C
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_002516.4(NOVA2):c.1104_1134delCGGGGCGGGCGGCGGGGCGGGCGGAGGGGGC(p.Gly369AlafsTer17) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_002516.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOVA2 | NM_002516.4 | c.1104_1134delCGGGGCGGGCGGCGGGGCGGGCGGAGGGGGC | p.Gly369AlafsTer17 | frameshift_variant | Exon 4 of 4 | ENST00000263257.6 | NP_002507.1 | |
NOVA2 | XM_006723230.4 | c.777_807delCGGGGCGGGCGGCGGGGCGGGCGGAGGGGGC | p.Gly260AlafsTer17 | frameshift_variant | Exon 5 of 5 | XP_006723293.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOVA2 | ENST00000263257.6 | c.1104_1134delCGGGGCGGGCGGCGGGGCGGGCGGAGGGGGC | p.Gly369AlafsTer17 | frameshift_variant | Exon 4 of 4 | 1 | NM_002516.4 | ENSP00000263257.4 | ||
NOVA2 | ENST00000676183.1 | c.1296_1326delCGGGGCGGGCGGCGGGGCGGGCGGAGGGGGC | p.Gly433AlafsTer17 | frameshift_variant | Exon 4 of 4 | ENSP00000501708.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
NOVA2-related disorder Pathogenic:1
The NOVA2 c.1104_1134del31 variant is predicted to result in a frameshift and premature protein termination (p.Gly369Alafs*17). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. However, frameshift variants in NOVA2 are expected to be pathogenic (see, for example, Mattioli et al. 2020. PubMed ID: 32197073; Scala et al. 2022. PubMed ID: 35607920). Taken together, this variant is interpreted as likely pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.