Genetic Variant ZNF233:p.Ile104Arg (chr19-44272971-T-G) – 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_001207005.2(ZNF233):c.311T>G(p.Ile104Arg) 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. I104T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

ZNF233
NM_001207005.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.92

Publications

1 publications found

Variant links:

Genes affected

ZNF233 (HGNC:30946): (zinc finger protein 233) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF233 links:

ZNF235 (HGNC:12866): (zinc finger protein 235) This gene product belongs to the zinc finger protein superfamily, members of which are regulatory proteins characterized by nucleic acid-binding zinc finger domains. The encoded protein is a member of the Kruppel family of zinc finger proteins, and contains Kruppel-associated box (KRAB) A and B domains and 15 tandemly arrayed C2H2-type zinc fingers. It is an ortholog of the mouse Zfp93 protein. This gene is located in a cluster of zinc finger genes on 19q13.2. [provided by RefSeq, Jul 2008]

ZNF235 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=0.07017425).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001207005.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ZNF233	NM_001207005.2	MANE Select	c.311T>G	p.Ile104Arg	missense	Exon 5 of 5	NP_001193934.1	A6NK53
ZNF233	NM_181756.3		c.311T>G	p.Ile104Arg	missense	Exon 5 of 5	NP_861421.2	A6NK53
ZNF233	NM_001330529.2		c.*71T>G		3_prime_UTR	Exon 5 of 5	NP_001317458.1	K7ER86

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ZNF233	ENST00000683810.1	MANE Select	c.311T>G	p.Ile104Arg	missense	Exon 5 of 5	ENSP00000507588.1	A6NK53
ZNF235	ENST00000589799.5	TSL:1	c.238+25837A>C		intron	N/A	ENSP00000468695.1	K7ESF8
ZNF233	ENST00000391958.6	TSL:2	c.311T>G	p.Ile104Arg	missense	Exon 5 of 5	ENSP00000375820.1	A6NK53

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000400

AC:

AN:

250102

AF XY:

0.00000739

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000545

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ExAC

AF:

0.00000824

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.67

CADD

Benign

1.5

(source)

DANN

Benign

0.95

DEOGEN2

Benign

0.0017

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.027

LIST_S2

Benign

0.70

M_CAP

Benign

0.0016

MetaRNN

Benign

0.070

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.55

PhyloP100

-2.9

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.30

REVEL

Benign

0.013

Sift

Benign

0.051

Sift4G

Benign

0.17

Polyphen

0.0010

Vest4

0.24

MutPred

0.41

Gain of solvent accessibility (P = 0.0367)

MVP

0.055

MPC

0.14

ClinPred

0.036

GERP RS

0.29

Varity_R

0.068

gMVP

0.26

Mutation Taster

=100/0

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

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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