19-45937042-A-G

Position:

• chr19-45937042-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002516.4(NOVA2):​c.*2821T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,980 control chromosomes in the GnomAD database, including 24,084 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.55 (24080 hom., cov: 30)
  • Exomes 𝑓: 0.44 (4 hom.)
• Consequence: NOVA2 NM_002516.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NOVA2	NM_002516.4	c.*2821T>C		3_prime_UTR_variant	4/4	ENST00000263257.6	NP_002507.1
NOVA2	XM_006723230.4	c.*2821T>C		3_prime_UTR_variant	5/5		XP_006723293.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NOVA2	ENST00000263257	c.*2821T>C		3_prime_UTR_variant	4/4	1	NM_002516.4	ENSP00000263257.4
NOVA2	ENST00000676183	c.*2821T>C		3_prime_UTR_variant	4/4			ENSP00000501708.1

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84270 AN: 151828 Hom.: 24070 Cov.: 30

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.526

GnomAD4 exome AF: 0.441 AC: 15 AN: 34 Hom.: 4 Cov.: 0 AF XY: 0.409 AC XY: 9 AN XY: 22

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.555 AC: 84307 AN: 151946 Hom.: 24080 Cov.: 30 AF XY: 0.558 AC XY: 41450 AN XY: 74266

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.530

Alfa AF: 0.577 Hom.: 35233

Bravo AF: 0.526

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.76

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: rs1990932; hg19: chr19-46440300;