19-9653745-C-G

Variant summary

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

The NM_001130031.2(ZNF562):​c.485G>C​(p.Ser162Thr) 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. 15/21 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. S162I) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ZNF562
NM_001130031.2 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.161
Variant links:
Genes affected
ZNF562 (HGNC:25950): (zinc finger protein 562) 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]
ZNF561-AS1 (HGNC:27613): (ZNF561 antisense RNA 1 (head to head))

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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=0.082060665).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF562NM_001130031.2 linkc.485G>C p.Ser162Thr missense_variant Exon 6 of 6 ENST00000453372.7 NP_001123503.1 Q6V9R5-1A0A024R7A3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF562ENST00000453372.7 linkc.485G>C p.Ser162Thr missense_variant Exon 6 of 6 3 NM_001130031.2 ENSP00000410734.1 Q6V9R5-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1461790
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
727190
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.078
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.71
CADD
Benign
2.0
DANN
Benign
0.18
DEOGEN2
Benign
0.0047
.;T;T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.0088
N
LIST_S2
Benign
0.35
T;T;T
M_CAP
Benign
0.00074
T
MetaRNN
Benign
0.082
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.69
.;N;.
PrimateAI
Benign
0.25
T
PROVEAN
Benign
-0.040
N;N;.
REVEL
Benign
0.025
Sift
Benign
0.42
T;T;.
Sift4G
Benign
0.23
T;T;T
Polyphen
0.0
B;B;.
Vest4
0.056
MutPred
0.35
.;Loss of disorder (P = 0.0616);.;
MVP
0.13
ClinPred
0.016
T
GERP RS
1.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.021
gMVP
0.029

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: chr19-9764421; API