chr16-30583183-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152458.7(ZNF785):c.595C>T(p.Pro199Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000062 in 1,613,976 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)
Exomes 𝑓: 0.0000062 ( 0 hom. )
Consequence
ZNF785
NM_152458.7 missense
NM_152458.7 missense
Scores
3
4
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.52
Genes affected
ZNF785 (HGNC:26496): (zinc finger protein 785) 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]
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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=0.24946746).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF785 | NM_152458.7 | c.595C>T | p.Pro199Ser | missense_variant | 3/3 | ENST00000395216.3 | |
ZNF785 | XM_011545753.3 | c.634C>T | p.Pro212Ser | missense_variant | 3/4 | ||
ZNF785 | XM_017022967.3 | c.595C>T | p.Pro199Ser | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF785 | ENST00000395216.3 | c.595C>T | p.Pro199Ser | missense_variant | 3/3 | 1 | NM_152458.7 | P2 | |
ENST00000492040.1 | n.811G>A | non_coding_transcript_exon_variant | 2/2 | 1 | |||||
ZNF785 | ENST00000470110.2 | c.550C>T | p.Pro184Ser | missense_variant | 3/4 | 2 | A2 | ||
ZNF785 | ENST00000567773.1 | c.*302C>T | 3_prime_UTR_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461748Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727166
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74368
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Benign
Sift
Benign
T;T
Sift4G
Pathogenic
D;D
Polyphen
P;P
Vest4
MutPred
0.34
.;Loss of catalytic residue at P199 (P = 0.0395);
MVP
MPC
1.2
ClinPred
D
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at