rs9326506

chr10-43573110-A-C

Variant summary

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

The NM_001099282.2(ZNF239):c.-216+527T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,018 control chromosomes in the GnomAD database, including 16,424 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 0.45 (16424 hom., cov: 32)
• Consequence: ZNF239 NM_001099282.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF239	NM_001099282.2	c.-216+527T>G		intron_variant		ENST00000374446.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF239	ENST00000374446.7	c.-216+527T>G		intron_variant		1	NM_001099282.2	P1
ZNF239	ENST00000426961.1	c.-216+1430T>G		intron_variant		2		P1
ZNF239	ENST00000535642.5	c.-93+1430T>G		intron_variant		2		P1
ZNF239	ENST00000491188.1	n.58+1430T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67662 AN: 151900 Hom.: 16420 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.445 AC: 67689 AN: 152018 Hom.: 16424 Cov.: 32 AF XY: 0.452 AC XY: 33577 AN XY: 74290

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.473

Alfa AF: 0.481 Hom.: 5811

Bravo AF: 0.427

Asia WGS AF: 0.546 AC: 1902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	10
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9326506; hg19: chr10-44068558;