chr10-43564228-C-A

Variant names:

• chr10-43564228-C-A
• rs1338565
• NM_001099282.2:c.-93+3671G>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.-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
• 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF239	NM_001099282.2	c.-93+3671G>T		intron_variant	Intron 3 of 3	ENST00000374446.7	NP_001092752.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF239	ENST00000374446.7	c.-93+3671G>T		intron_variant	Intron 3 of 3	1	NM_001099282.2	ENSP00000363569.1

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

African (AFR) AF: 0.510 AC: 7520 AN: 14738

American (AMR) AF: 0.487 AC: 446 AN: 916

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 2307 AN: 4814

East Asian (EAS) AF: 0.537 AC: 1797 AN: 3344

South Asian (SAS) AF: 0.614 AC: 9406 AN: 15324

European-Finnish (FIN) AF: 0.657 AC: 176 AN: 268

Middle Eastern (MID) AF: 0.599 AC: 922 AN: 1538

European-Non Finnish (NFE) AF: 0.529 AC: 376405 AN: 711948

Other (OTH) AF: 0.530 AC: 13465 AN: 25408

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

African (AFR) AF: 0.503 AC: 20816 AN: 41412

American (AMR) AF: 0.507 AC: 7738 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1633 AN: 3470

East Asian (EAS) AF: 0.549 AC: 2822 AN: 5144

South Asian (SAS) AF: 0.608 AC: 2931 AN: 4818

European-Finnish (FIN) AF: 0.628 AC: 6642 AN: 10570

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.541 AC: 36740 AN: 67944

Other (OTH) AF: 0.543 AC: 1146 AN: 2112

Alfa AF: 0.514 Hom.: 6028

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
PhyloP100		0.043
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: rs1338565; hg19: chr10-44059676;