19-45940559-CA-C

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_Strong PM2 PP5_Moderate

The NM_002516.4(NOVA2):c.782del(p.Val261GlyfsTer135) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 34)
• Consequence: NOVA2 NM_002516.4 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 8.07

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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.471 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 19-45940559-CA-C is Pathogenic according to our data. Variant chr19-45940559-CA-C is described in ClinVar as [Pathogenic]. Clinvar id is 812085.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-45940559-CA-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOVA2	NM_002516.4	c.782del	p.Val261GlyfsTer135	frameshift_variant	4/4	ENST00000263257.6
NOVA2	XM_006723230.4	c.455del	p.Val152GlyfsTer135	frameshift_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOVA2	ENST00000263257.6	c.782del	p.Val261GlyfsTer135	frameshift_variant	4/4	1	NM_002516.4	P1
NOVA2	ENST00000676183.1	c.974del	p.Val325GlyfsTer135	frameshift_variant	4/4

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 61

GnomAD4 genome Cov.: 34

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Apr 30, 2020

- -

Intellectual disability, severe Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Diagnostic Laboratory, Strasbourg University Hospital

Sep 26, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1600596180; hg19: chr19-46443817;