Variant 19-55602288-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_153219.4(ZNF524):c.176A>G(p.Lys59Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000697 in 1,434,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 7.0e-7 ( 0 hom. )

Consequence

ZNF524
NM_153219.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.237

Variant links:

Genes affected

ZNF524 (HGNC:28322): (zinc finger protein 524) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF524 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.050083727).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF524	NM_153219.4 linkuse as main transcript	c.176A>G	p.Lys59Arg	missense_variant	2/2	ENST00000301073.4	NP_694951.1	Q96C55
ZNF524	XM_011526487.3 linkuse as main transcript	c.494A>G	p.Lys165Arg	missense_variant	2/2		XP_011524789.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZNF524	ENST00000301073.4 linkuse as main transcript	c.176A>G	p.Lys59Arg	missense_variant	2/2	1	NM_153219.4	ENSP00000301073.2	Q96C55
ZNF524	ENST00000591046.1 linkuse as main transcript	c.176A>G	p.Lys59Arg	missense_variant	1/1	6		ENSP00000466907.1	Q96C55
ZNF524	ENST00000589521.1 linkuse as main transcript	c.176A>G	p.Lys59Arg	missense_variant	2/2	3		ENSP00000467175.1	K7EP10

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.97e-7

AC:

AN:

1434770

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

711552

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000121

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 21, 2022

The c.176A>G (p.K59R) alteration is located in exon 2 (coding exon 1) of the ZNF524 gene. This alteration results from a A to G substitution at nucleotide position 176, causing the lysine (K) at amino acid position 59 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Benign

0.49

DEOGEN2

Benign

0.010

T;T;T

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.017

LIST_S2

Benign

0.50

T;.;T

M_CAP

Benign

0.0026

MetaRNN

Benign

0.050

T;T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

0.34

.;N;N

PrimateAI

Benign

0.42

PROVEAN

Benign

-0.46

.;N;.

REVEL

Benign

0.020

Sift

Benign

0.58

.;T;.

Sift4G

Benign

0.64

T;T;T

Polyphen

0.0030

.;B;B

Vest4

0.078, 0.081

MutPred

0.33

Loss of methylation at K59 (P = 0.0056);Loss of methylation at K59 (P = 0.0056);Loss of methylation at K59 (P = 0.0056);

MVP

0.19

MPC

0.32

ClinPred

0.017

GERP RS

-1.1

Varity_R

0.023

gMVP

0.19

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over