chr19-45940481-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002516.4(NOVA2):c.861A>C(p.Ala287=) variant causes a synonymous change. The variant allele was found at a frequency of 0.701 in 1,530,170 control chromosomes in the GnomAD database, including 378,245 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.72 ( 39861 hom., cov: 33)
Exomes 𝑓: 0.70 ( 338384 hom. )
Consequence
NOVA2
NM_002516.4 synonymous
NM_002516.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.10
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant 19-45940481-T-G is Benign according to our data. Variant chr19-45940481-T-G is described in ClinVar as [Benign]. Clinvar id is 1326984.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOVA2 | NM_002516.4 | c.861A>C | p.Ala287= | synonymous_variant | 4/4 | ENST00000263257.6 | |
NOVA2 | XM_006723230.4 | c.534A>C | p.Ala178= | synonymous_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOVA2 | ENST00000263257.6 | c.861A>C | p.Ala287= | synonymous_variant | 4/4 | 1 | NM_002516.4 | P1 | |
NOVA2 | ENST00000676183.1 | c.1053A>C | p.Ala351= | synonymous_variant | 4/4 |
Frequencies
GnomAD3 genomes ? AF: 0.723 AC: 108776AN: 150510Hom.: 39826 Cov.: 33
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GnomAD3 exomes AF: 0.678 AC: 120952AN: 178450Hom.: 41864 AF XY: 0.682 AC XY: 68081AN XY: 99782
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GnomAD4 exome AF: 0.699 AC: 963682AN: 1379552Hom.: 338384 Cov.: 65 AF XY: 0.699 AC XY: 478726AN XY: 685316
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GnomAD4 genome ? AF: 0.723 AC: 108856AN: 150618Hom.: 39861 Cov.: 33 AF XY: 0.724 AC XY: 53232AN XY: 73546
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at