rs1338565

chr10-43564228-C-Achr10-43564228-C-G

Variant summary

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

The NM_001099282.2(ZNF239):c.-93+3671G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 930,242 control chromosomes in the GnomAD database, including 131,886 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 0.53 (21934 hom., cov: 31)
  • Exomes 𝑓: 0.53 (109952 hom.)
• Consequence: ZNF239 NM_001099282.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

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=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF239	NM_001099282.2	c.-93+3671G>T		intron_variant		ENST00000374446.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF239	ENST00000374446.7	c.-93+3671G>T		intron_variant		1	NM_001099282.2	P1

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81087 AN: 151826 Hom.: 21918 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.538

GnomAD4 exome AF: 0.530 AC: 412444 AN: 778298 Hom.: 109952 Cov.: 11 AF XY: 0.529 AC XY: 191162 AN XY: 361044

Gnomad4 AFR exome AF: 0.510

Gnomad4 AMR exome AF: 0.487

Gnomad4 ASJ exome AF: 0.479

Gnomad4 EAS exome AF: 0.537

Gnomad4 SAS exome AF: 0.614

Gnomad4 FIN exome AF: 0.657

Gnomad4 NFE exome AF: 0.529

Gnomad4 OTH exome AF: 0.530

GnomAD4 genome AF: 0.534 AC: 81151 AN: 151944 Hom.: 21934 Cov.: 31 AF XY: 0.539 AC XY: 40004 AN XY: 74252

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.543

Alfa AF: 0.481 Hom.: 2870

Bravo AF: 0.525

Asia WGS AF: 0.605 AC: 2106 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	7.0
Dann	Benign	0.90

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: rs1338565; hg19: chr10-44059676;