rs10793442

Positions:

• chr10-43556371-C-A

Variant summary

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

The ENST00000374446.7(ZNF239):​c.*332G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 235,038 control chromosomes in the GnomAD database, including 3,599 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 (2175 hom., cov: 32)
  • Exomes 𝑓: 0.16 (1424 hom.)
• Consequence: ZNF239 ENST00000374446.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

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=-0.74).
• 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	Protein	UniProt
ZNF239	NM_001099282.2	c.*332G>T		3_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.*332G>T		3_prime_UTR_variant	4/4	1	NM_001099282.2	ENSP00000363569	P1
ZNF239	ENST00000306006.10	c.*332G>T		3_prime_UTR_variant	2/2	1		ENSP00000307774	P1
ZNF239	ENST00000426961.1	c.*332G>T		3_prime_UTR_variant	3/3	2		ENSP00000398202	P1
ZNF239	ENST00000535642.5	c.*332G>T		3_prime_UTR_variant	2/2	2		ENSP00000443907	P1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23440 AN: 151960 Hom.: 2180 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.162

GnomAD4 exome AF: 0.156 AC: 12946 AN: 82962 Hom.: 1424 Cov.: 1 AF XY: 0.158 AC XY: 6714 AN XY: 42610

Gnomad4 AFR exome AF: 0.130

Gnomad4 AMR exome AF: 0.237

Gnomad4 ASJ exome AF: 0.111

Gnomad4 EAS exome AF: 0.447

Gnomad4 SAS exome AF: 0.175

Gnomad4 FIN exome AF: 0.128

Gnomad4 NFE exome AF: 0.120

Gnomad4 OTH exome AF: 0.138

GnomAD4 genome AF: 0.154 AC: 23446 AN: 152076 Hom.: 2175 Cov.: 32 AF XY: 0.161 AC XY: 11945 AN XY: 74320

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.160

Alfa AF: 0.134 Hom.: 1592

Bravo AF: 0.158

Asia WGS AF: 0.282 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.6
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: rs10793442; hg19: chr10-44051819;