rs568515212

Variant summary

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

The NM_020951.5(ZNF529):​c.1148G>T​(p.Arg383Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,612,922 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 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. R383H) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

ZNF529
NM_020951.5 missense

Scores

1
1
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -6.58
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=0.115410745).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF529NM_020951.5 linkc.1148G>T p.Arg383Leu 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.1148G>T p.Arg383Leu missense_variant Exon 5 of 5 1 NM_020951.5 ENSP00000465578.1 Q6P280
ZNF529ENST00000334116.7 linkc.833G>T p.Arg278Leu missense_variant Exon 6 of 6 2 ENSP00000334695.7 A0A0C4DFR4
ZNF529ENST00000590656.1 linkc.119G>T p.Arg40Leu missense_variant Exon 1 of 3 3 ENSP00000468594.1 K7ES80
ZNF529ENST00000452073.2 linkc.205+148G>T intron_variant Intron 1 of 1 3 ENSP00000465917.1 K7EL49

Frequencies

GnomAD3 genomes
AF:
0.00000660
AC:
1
AN:
151410
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
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:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000800
AC:
2
AN:
249970
Hom.:
0
AF XY:
0.00000738
AC XY:
1
AN XY:
135538
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000177
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461512
Hom.:
0
Cov.:
34
AF XY:
0.00000138
AC XY:
1
AN XY:
727034
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000660
AC:
1
AN:
151410
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
73910
show subpopulations
Gnomad4 AFR
AF:
0.00
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:
0.0000147
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000378
ExAC
AF:
0.0000165
AC:
2
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.88
BayesDel_addAF
Benign
-0.29
T
BayesDel_noAF
Benign
-0.64
CADD
Benign
12
DANN
Benign
0.93
DEOGEN2
Benign
0.025
.;T;T
Eigen
Benign
-0.75
Eigen_PC
Benign
-0.73
FATHMM_MKL
Benign
0.0
N
LIST_S2
Benign
0.63
T;T;T
M_CAP
Benign
0.0038
T
MetaRNN
Benign
0.12
T;T;T
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
1.1
.;.;L
PrimateAI
Uncertain
0.53
T
REVEL
Benign
0.042
Sift4G
Benign
0.13
T;T;T
Vest4
0.13, 0.31
MVP
0.39
MPC
0.63
ClinPred
0.71
D
GERP RS
0.64
Varity_R
0.074
gMVP
0.10

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: rs568515212; hg19: chr19-37038312; COSMIC: COSV61901686; COSMIC: COSV61901686; API