10-43564228-C-G

Variant names:

• chr10-43564228-C-G
• rs1338565
• NM_001099282.2:c.-93+3671G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001099282.2(ZNF239):​c.-93+3671G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF239 NM_001099282.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 3 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).

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.-93+3671G>C		intron	N/A	NP_001092752.1	Q16600
	ZNF239	NM_001324353.2		c.247+3671G>C		intron	N/A	NP_001311282.1
	ZNF239	NM_001324352.2		c.34+3667G>C		intron	N/A	NP_001311281.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF239	ENST00000374446.7	TSL:1 MANE Select	c.-93+3671G>C		intron	N/A	ENSP00000363569.1	Q16600
	ZNF239	ENST00000306006.10	TSL:1	c.-93+3671G>C		intron	N/A	ENSP00000307774.6	Q16600
	ZNF239	ENST00000426961.1	TSL:2	c.-93+3671G>C		intron	N/A	ENSP00000398202.1	Q16600

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 780632 Hom.: 0 Cov.: 11 AF XY: 0.00 AC XY: 0 AN XY: 362102

African (AFR) AF: 0.00 AC: 0 AN: 14772

American (AMR) AF: 0.00 AC: 0 AN: 918

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4828

East Asian (EAS) AF: 0.00 AC: 0 AN: 3358

South Asian (SAS) AF: 0.00 AC: 0 AN: 15362

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 270

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1542

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 714102

Other (OTH) AF: 0.00 AC: 0 AN: 25480

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 6028

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.3
DANN	Benign	0.84
PhyloP100		0.043

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: rs1338565; hg19: chr10-44059676;