rs1433132044

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001098626.2(ZNF98):​c.1571G>T​(p.Gly524Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. G524D) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

ZNF98
NM_001098626.2 missense

Scores

4
2
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.323
Variant links:
Genes affected
ZNF98 (HGNC:13174): (zinc finger protein 98) 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, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF98NM_001098626.2 linkc.1571G>T p.Gly524Val missense_variant Exon 4 of 4 ENST00000357774.9 NP_001092096.1 A6NK75

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF98ENST00000357774.9 linkc.1571G>T p.Gly524Val missense_variant Exon 4 of 4 1 NM_001098626.2 ENSP00000350418.4 A6NK75

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.66
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
18
DANN
Benign
0.96
DEOGEN2
Benign
0.29
T
Eigen
Benign
-0.32
Eigen_PC
Benign
-0.70
FATHMM_MKL
Benign
0.055
N
LIST_S2
Benign
0.026
T
M_CAP
Benign
0.0042
T
MetaRNN
Uncertain
0.47
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Pathogenic
3.6
H
PrimateAI
Benign
0.27
T
PROVEAN
Pathogenic
-7.1
D
REVEL
Benign
0.092
Sift
Pathogenic
0.0
D
Sift4G
Uncertain
0.013
D
Polyphen
1.0
D
Vest4
0.26
MutPred
0.66
Loss of disorder (P = 0.0255);
MVP
0.45
MPC
2.1
ClinPred
0.97
D
GERP RS
-1.9
Varity_R
0.46
gMVP
0.023

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-22574466; API