chr10-43573110-A-C

Variant names:

• chr10-43573110-A-C
• rs9326506
• NM_001099282.2:c.-216+527T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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=-0.84).
• 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 rank	MANE	Protein	UniProt
ZNF239	NM_001099282.2	c.-216+527T>G		intron_variant	Intron 2 of 3	ENST00000374446.7	NP_001092752.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF239	ENST00000374446.7	c.-216+527T>G		intron_variant	Intron 2 of 3	1	NM_001099282.2	ENSP00000363569.1
ZNF239	ENST00000426961.1	c.-216+1430T>G		intron_variant	Intron 1 of 2	2		ENSP00000398202.1
ZNF239	ENST00000535642.5	c.-93+1430T>G		intron_variant	Intron 1 of 1	2		ENSP00000443907.1
ZNF239	ENST00000491188.1	n.58+1430T>G		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.246 AC: 10184 AN: 41480

American (AMR) AF: 0.468 AC: 7146 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1616 AN: 3466

East Asian (EAS) AF: 0.539 AC: 2777 AN: 5152

South Asian (SAS) AF: 0.546 AC: 2632 AN: 4822

European-Finnish (FIN) AF: 0.612 AC: 6459 AN: 10562

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35201 AN: 67950

Other (OTH) AF: 0.473 AC: 1000 AN: 2116

Alfa AF: 0.480 Hom.: 7178

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
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs9326506; hg19: chr10-44068558;