19-45940342-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002516.4(NOVA2):c.1000G>A(p.Ala334Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000102 in 1,277,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002516.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOVA2 | ENST00000263257.6 | c.1000G>A | p.Ala334Thr | missense_variant | Exon 4 of 4 | 1 | NM_002516.4 | ENSP00000263257.4 | ||
NOVA2 | ENST00000676183.1 | c.1192G>A | p.Ala398Thr | missense_variant | Exon 4 of 4 | ENSP00000501708.1 |
Frequencies
GnomAD3 genomes AF: 0.0000201 AC: 3AN: 149218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000297 AC: 7AN: 23584Hom.: 0 AF XY: 0.000275 AC XY: 4AN XY: 14530
GnomAD4 exome AF: 0.00000887 AC: 10AN: 1127932Hom.: 0 Cov.: 30 AF XY: 0.0000109 AC XY: 6AN XY: 549148
GnomAD4 genome AF: 0.0000201 AC: 3AN: 149218Hom.: 0 Cov.: 32 AF XY: 0.0000275 AC XY: 2AN XY: 72708
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1000G>A (p.A334T) alteration is located in exon 4 (coding exon 4) of the NOVA2 gene. This alteration results from a G to A substitution at nucleotide position 1000, causing the alanine (A) at amino acid position 334 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
NOVA2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at