10-43558137-C-T

Position:

• chr10-43558137-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001324353.2(ZNF239):​c.282G>A​(p.Gln94Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 1,524,316 control chromosomes in the GnomAD database, including 222,535 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 0.54 (22110 hom., cov: 32)
  • Exomes 𝑓: 0.54 (200425 hom.)
• Consequence: ZNF239 NM_001324353.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

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]

ZNF239 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP7: Synonymous conserved (PhyloP=-0.324 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF239	NM_001099282.2	c.-58G>A		5_prime_UTR_variant	4/4	ENST00000374446.7	NP_001092752.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF239	ENST00000374446.7	c.-58G>A		5_prime_UTR_variant	4/4	1	NM_001099282.2	ENSP00000363569.1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81412 AN: 151910 Hom.: 22091 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.539

GnomAD4 exome AF: 0.540 AC: 740616 AN: 1372288 Hom.: 200425 Cov.: 40 AF XY: 0.541 AC XY: 364959 AN XY: 674126

Gnomad4 AFR exome AF: 0.516

Gnomad4 AMR exome AF: 0.505

Gnomad4 ASJ exome AF: 0.477

Gnomad4 EAS exome AF: 0.553

Gnomad4 SAS exome AF: 0.610

Gnomad4 FIN exome AF: 0.624

Gnomad4 NFE exome AF: 0.533

Gnomad4 OTH exome AF: 0.538

GnomAD4 genome AF: 0.536 AC: 81483 AN: 152028 Hom.: 22110 Cov.: 32 AF XY: 0.541 AC XY: 40164 AN XY: 74294

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.544

Alfa AF: 0.534 Hom.: 10360

Bravo AF: 0.527

Asia WGS AF: 0.604 AC: 2101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	9.3
DANN	Benign	0.73

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: rs2999278; hg19: chr10-44053585; COSMIC: COSV60018588;