rs3763789

Variant names:

• chr10-43565912-A-G
• rs3763789
• NM_001099282.2:c.-93+1987T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF239	NM_001099282.2	c.-93+1987T>C		intron_variant	Intron 3 of 3	ENST00000374446.7	NP_001092752.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF239	ENST00000374446.7	c.-93+1987T>C		intron_variant	Intron 3 of 3	1	NM_001099282.2	ENSP00000363569.1

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

African (AFR) AF: 0.124 AC: 5140 AN: 41394

American (AMR) AF: 0.218 AC: 3324 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2314 AN: 5154

South Asian (SAS) AF: 0.191 AC: 913 AN: 4788

European-Finnish (FIN) AF: 0.159 AC: 1654 AN: 10382

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8667 AN: 67894

Other (OTH) AF: 0.158 AC: 331 AN: 2098

Alfa AF: 0.131 Hom.: 646

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
PhyloP100		1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3763789; hg19: chr10-44061360;