chr10-43557268-C-A

Variant names:

• chr10-43557268-C-A
• NM_001099282.2:c.812G>T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001099282.2(ZNF239):​c.812G>T​(p.Gly271Val) variant causes a missense 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G271D) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ZNF239 NM_001099282.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

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 Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2840354).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF239	NM_001099282.2	c.812G>T	p.Gly271Val	missense_variant	Exon 4 of 4	ENST00000374446.7	NP_001092752.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF239	ENST00000374446.7	c.812G>T	p.Gly271Val	missense_variant	Exon 4 of 4	1	NM_001099282.2	ENSP00000363569.1
ZNF239	ENST00000306006.10	c.812G>T	p.Gly271Val	missense_variant	Exon 2 of 2	1		ENSP00000307774.6
ZNF239	ENST00000426961.1	c.812G>T	p.Gly271Val	missense_variant	Exon 3 of 3	2		ENSP00000398202.1
ZNF239	ENST00000535642.5	c.812G>T	p.Gly271Val	missense_variant	Exon 2 of 2	2		ENSP00000443907.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.59
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.43
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.055	T;T;T;T
Eigen	Benign	0.16
Eigen_PC	Benign	0.099
FATHMM_MKL	Benign	0.19	N
LIST_S2	Benign	0.31	.;.;.;T
M_CAP	Benign	0.0026	T
MetaRNN	Benign	0.28	T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.63	N;N;N;N
PrimateAI	Uncertain	0.58	T
PROVEAN	Uncertain	-3.7	D;D;D;D
REVEL	Benign	0.23
Sift	Benign	0.085	T;T;T;T
Sift4G	Uncertain	0.018	D;D;D;D
Polyphen		1.0	D;D;D;D
Vest4		0.35
MutPred		0.39		Loss of disorder (P = 0.0379);Loss of disorder (P = 0.0379);Loss of disorder (P = 0.0379);Loss of disorder (P = 0.0379);
MVP		0.28
MPC		0.35
ClinPred		0.96	D
GERP RS		3.8
Varity_R		0.41
gMVP		0.037

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-44052716;