Genetic Variant ZNF212:p.Pro6Leu (chr7-149239795-C-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_012256.4(ZNF212):c.17C>T(p.Pro6Leu) 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. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P6S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ZNF212
NM_012256.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.52

Publications

0 publications found

Variant links:

Genes affected

ZNF212 (HGNC:13004): (zinc finger protein 212) This gene belongs to the C2H2-type zinc finger gene family. The zinc finger proteins are involved in gene regulation and development, and are quite conserved throughout evolution. Like this gene product, a third of the zinc finger proteins containing C2H2 fingers also contain the KRAB domain, which has been found to be involved in protein-protein interactions. [provided by RefSeq, Jul 2008]

ZNF212 links:

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ACMG classification

Classification was made for transcript

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=0.21688256).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012256.4. 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
	ZNF212	NM_012256.4	MANE Select	c.17C>T	p.Pro6Leu	missense	Exon 1 of 5	NP_036388.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ZNF212	ENST00000335870.7	TSL:1 MANE Select	c.17C>T	p.Pro6Leu	missense	Exon 1 of 5	ENSP00000338572.2	Q9UDV6
ZNF212	ENST00000877956.1		c.17C>T	p.Pro6Leu	missense	Exon 1 of 5	ENSP00000548015.1
ZNF212	ENST00000462724.1	TSL:5	n.17C>T		non_coding_transcript_exon	Exon 1 of 3	ENSP00000418167.1	F2Z3G9

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1122002

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

533256

African (AFR)

AF:

0.00

AC:

AN:

24158

American (AMR)

AF:

0.00

AC:

AN:

11112

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14670

East Asian (EAS)

AF:

0.00

AC:

AN:

28468

South Asian (SAS)

AF:

0.00

AC:

AN:

23070

European-Finnish (FIN)

AF:

0.00

AC:

AN:

37474

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3788

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

934402

Other (OTH)

AF:

0.00

AC:

AN:

44860

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

BayesDel_addAF

Benign

-0.13

BayesDel_noAF

Benign

-0.43

CADD

Uncertain

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.13

Eigen

Uncertain

0.29

Eigen_PC

Uncertain

0.35

FATHMM_MKL

Benign

0.58

LIST_S2

Benign

0.68

M_CAP

Benign

0.010

MetaRNN

Benign

0.22

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.0

PhyloP100

2.5

PrimateAI

Uncertain

0.56

PROVEAN

Uncertain

-4.1

REVEL

Benign

0.072

Sift

Uncertain

0.0030

Sift4G

Pathogenic

0.0

Polyphen

0.94

Vest4

0.28

MutPred

0.28

Loss of glycosylation at P6 (P = 0.0239)

MVP

0.33

MPC

0.26

ClinPred

0.79

GERP RS

4.7

PromoterAI

-0.024

Neutral

(source)

Varity_R

0.27

gMVP

0.30

Mutation Taster

=88/12

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over