NM_020951.5:c.1155G>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_020951.5(ZNF529):​c.1155G>C​(p.Gln385His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)

Consequence

ZNF529
NM_020951.5 missense

Scores

1
3
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.146
Variant links:
Genes affected
ZNF529 (HGNC:29328): (zinc finger protein 529) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.11026552).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF529NM_020951.5 linkc.1155G>C p.Gln385His missense_variant Exon 5 of 5 ENST00000591340.6 NP_066002.3 Q6P280

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF529ENST00000591340.6 linkc.1155G>C p.Gln385His missense_variant Exon 5 of 5 1 NM_020951.5 ENSP00000465578.1 Q6P280
ZNF529ENST00000334116.7 linkc.840G>C p.Gln280His missense_variant Exon 6 of 6 2 ENSP00000334695.7 A0A0C4DFR4
ZNF529ENST00000590656.1 linkc.126G>C p.Gln42His missense_variant Exon 1 of 3 3 ENSP00000468594.1 K7ES80
ZNF529ENST00000452073.2 linkc.205+155G>C intron_variant Intron 1 of 1 3 ENSP00000465917.1 K7EL49

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152168
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
34
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152168
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Feb 07, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1155G>C (p.Q385H) alteration is located in exon 6 (coding exon 4) of the ZNF529 gene. This alteration results from a G to C substitution at nucleotide position 1155, causing the glutamine (Q) at amino acid position 385 to be replaced by a histidine (H). 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
Pathogenic
0.63
BayesDel_addAF
Benign
-0.29
T
BayesDel_noAF
Benign
-0.65
CADD
Benign
15
DANN
Uncertain
0.99
DEOGEN2
Benign
0.084
.;T;T
Eigen
Benign
-0.71
Eigen_PC
Benign
-0.70
FATHMM_MKL
Benign
0.000030
N
LIST_S2
Benign
0.066
T;T;T
M_CAP
Benign
0.0035
T
MetaRNN
Benign
0.11
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.98
.;.;L
PrimateAI
Uncertain
0.55
T
REVEL
Benign
0.072
Sift4G
Uncertain
0.015
D;T;D
Vest4
0.17
MVP
0.30
MPC
0.31
ClinPred
0.61
D
GERP RS
-0.84
Varity_R
0.13
gMVP
0.080

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1211880019; hg19: chr19-37038305; API