rs3763789

chr10-43565912-A-G

Variant summary

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

The NM_001099282.2(ZNF239):c.-93+1987T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 151,608 control chromosomes in the GnomAD database, including 2,120 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 0.15 (2120 hom., cov: 31)
• Consequence: ZNF239 NM_001099282.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

Genes affected

ZNF239 (HGNC:13031): (zinc finger protein 239) MOK2 proteins are DNA- and RNA-binding proteins that are mainly associated with nuclear RNP components, including the nucleoli and extranucleolar structures (Arranz et al., 1997 [PubMed 9121460]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF239	NM_001099282.2	c.-93+1987T>C		intron_variant		ENST00000374446.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF239	ENST00000374446.7	c.-93+1987T>C		intron_variant		1	NM_001099282.2	P1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22940 AN: 151490 Hom.: 2124 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.159

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 22948 AN: 151608 Hom.: 2120 Cov.: 31 AF XY: 0.158 AC XY: 11693 AN XY: 74114

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.158

Alfa AF: 0.130 Hom.: 353

Bravo AF: 0.156

Asia WGS AF: 0.279 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.2
Dann	Benign	0.39

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: rs3763789; hg19: chr10-44061360;