NM_004220.3:c.439C>G

Variant names:

• chr16-3138457-C-G
• rs774347813
• NM_004220.3:c.439C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_004220.3(ZNF213):​c.439C>G​(p.Arg147Gly) 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. 16/22 in silico tools predict 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. R147Q) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ZNF213 NM_004220.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.57
• Publications: 3 publications found

Genes affected

ZNF213 (HGNC:13005): (zinc finger protein 213) C2H2 zinc finger proteins, such as ZNF213, have bipartite structures in which one domain binds DNA or RNA and the other modulates target gene expression.[supplied by OMIM, Apr 2004]

ZNF213-AS1 (HGNC:50505): (ZNF213 antisense RNA 1 (head to head))

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08732417).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF213	NM_004220.3	c.439C>G	p.Arg147Gly	missense_variant	Exon 3 of 6	ENST00000396878.8	NP_004211.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF213	ENST00000396878.8	c.439C>G	p.Arg147Gly	missense_variant	Exon 3 of 6	1	NM_004220.3	ENSP00000380087.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	19
DANN	Benign	0.94
DEOGEN2	Benign	0.053	T;T;T;T;.;T
Eigen	Benign	-0.66
Eigen_PC	Benign	-0.57
FATHMM_MKL	Benign	0.33	N
LIST_S2	Benign	0.12	.;.;.;T;T;T
M_CAP	Benign	0.0064	T
MetaRNN	Benign	0.087	T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N;N;N;N;.;.
PhyloP100		2.6
PrimateAI	Benign	0.28	T
PROVEAN	Benign	-1.4	.;N;.;N;.;.
REVEL	Benign	0.066
Sift	Benign	0.17	.;T;.;T;.;.
Sift4G	Benign	0.29	T;T;T;T;T;D
Polyphen		0.093	B;B;B;B;.;.
Vest4		0.28
MutPred		0.27		Gain of catalytic residue at S149 (P = 0.0245);Gain of catalytic residue at S149 (P = 0.0245);Gain of catalytic residue at S149 (P = 0.0245);Gain of catalytic residue at S149 (P = 0.0245);.;.;
MVP		0.32
MPC		0.25
ClinPred		0.21	T
GERP RS		4.9
Varity_R		0.16
gMVP		0.22

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: rs774347813; hg19: chr16-3188458;