16-31083850-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014699.4(ZNF646):c.*758C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 1,609,334 control chromosomes in the GnomAD database, including 141,029 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.45 ( 16799 hom., cov: 33)
Exomes 𝑓: 0.40 ( 124230 hom. )
Consequence
ZNF646
NM_014699.4 3_prime_UTR
NM_014699.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.71
Genes affected
ZNF646 (HGNC:29004): (zinc finger protein 646) 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]
PRSS53 (HGNC:34407): (serine protease 53) Predicted to enable serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF646 | ENST00000300850.5 | c.*758C>T | 3_prime_UTR_variant | Exon 3 of 3 | 1 | NM_014699.4 | ENSP00000300850.5 | |||
PRSS53 | ENST00000280606.7 | c.1643-41G>A | intron_variant | Intron 10 of 10 | 1 | NM_001039503.3 | ENSP00000280606.6 |
Frequencies
GnomAD3 genomes AF: 0.452 AC: 68654AN: 151922Hom.: 16761 Cov.: 33
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GnomAD3 exomes AF: 0.419 AC: 103847AN: 247982Hom.: 24527 AF XY: 0.430 AC XY: 57884AN XY: 134708
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GnomAD4 exome AF: 0.399 AC: 581963AN: 1457294Hom.: 124230 Cov.: 34 AF XY: 0.406 AC XY: 294554AN XY: 725046
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GnomAD4 genome AF: 0.452 AC: 68745AN: 152040Hom.: 16799 Cov.: 33 AF XY: 0.454 AC XY: 33715AN XY: 74322
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at