rs10793442

Variant names:

• chr10-43556371-C-A
• rs10793442
• NM_001099282.2:c.*332G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001099282.2(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 NM_001099282.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 17 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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099282.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF239	NM_001099282.2	MANE Select	c.*332G>T		3_prime_UTR	Exon 4 of 4	NP_001092752.1	Q16600
	ZNF239	NM_001324353.2		c.*332G>T		3_prime_UTR	Exon 5 of 5	NP_001311282.1
	ZNF239	NM_001324352.2		c.*332G>T		3_prime_UTR	Exon 4 of 4	NP_001311281.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF239	ENST00000374446.7	TSL:1 MANE Select	c.*332G>T		3_prime_UTR	Exon 4 of 4	ENSP00000363569.1	Q16600
	ZNF239	ENST00000306006.10	TSL:1	c.*332G>T		3_prime_UTR	Exon 2 of 2	ENSP00000307774.6	Q16600
	ZNF239	ENST00000426961.1	TSL:2	c.*332G>T		3_prime_UTR	Exon 3 of 3	ENSP00000398202.1	Q16600

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

African (AFR) AF: 0.130 AC: 446 AN: 3430

American (AMR) AF: 0.237 AC: 1151 AN: 4862

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 296 AN: 2664

East Asian (EAS) AF: 0.447 AC: 2728 AN: 6100

South Asian (SAS) AF: 0.175 AC: 990 AN: 5662

European-Finnish (FIN) AF: 0.128 AC: 416 AN: 3244

Middle Eastern (MID) AF: 0.100 AC: 34 AN: 340

European-Non Finnish (NFE) AF: 0.120 AC: 6237 AN: 51980

Other (OTH) AF: 0.138 AC: 648 AN: 4680

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

African (AFR) AF: 0.132 AC: 5477 AN: 41482

American (AMR) AF: 0.220 AC: 3360 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2320 AN: 5166

South Asian (SAS) AF: 0.197 AC: 950 AN: 4814

European-Finnish (FIN) AF: 0.162 AC: 1710 AN: 10564

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

European-Non Finnish (NFE) AF: 0.128 AC: 8686 AN: 67992

Other (OTH) AF: 0.160 AC: 338 AN: 2110

Alfa AF: 0.135 Hom.: 2120

Bravo AF: 0.158

Asia WGS AF: 0.282 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.6
DANN	Benign	0.76
PhyloP100		0.0010
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: rs10793442; hg19: chr10-44051819;