rs4281830
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152478.3(ZNF583):c.233-975G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 151,992 control chromosomes in the GnomAD database, including 22,547 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 0.54 ( 22547 hom., cov: 32)
Consequence
ZNF583
NM_152478.3 intron
NM_152478.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.23
Genes affected
ZNF583 (HGNC:26427): (zinc finger protein 583) 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 by RNA polymerase II. Predicted to be active in nucleus. [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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF583 | NM_152478.3 | c.233-975G>A | intron_variant | ENST00000333201.13 | NP_689691.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF583 | ENST00000333201.13 | c.233-975G>A | intron_variant | 2 | NM_152478.3 | ENSP00000388502 | P1 | |||
ZNF583 | ENST00000291598.11 | c.233-975G>A | intron_variant | 3 | ENSP00000291598 | P1 | ||||
ZNF583 | ENST00000391778.3 | c.233-975G>A | intron_variant | 4 | ENSP00000375657 | |||||
ZNF583 | ENST00000537943.5 | c.233-975G>A | intron_variant | 3 | ENSP00000444291 |
Frequencies
GnomAD3 genomes AF: 0.539 AC: 81815AN: 151874Hom.: 22520 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.539 AC: 81889AN: 151992Hom.: 22547 Cov.: 32 AF XY: 0.545 AC XY: 40464AN XY: 74302
GnomAD4 genome
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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