rs2173724
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001001415.4(ZNF429):c.4-3303A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,900 control chromosomes in the GnomAD database, including 2,639 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 0.19 ( 2639 hom., cov: 32)
Consequence
ZNF429
NM_001001415.4 intron
NM_001001415.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.164
Genes affected
ZNF429 (HGNC:20817): (zinc finger protein 429) 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=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF429 | ENST00000358491.9 | c.4-3303A>G | intron_variant | Intron 1 of 3 | 3 | NM_001001415.4 | ENSP00000351280.3 | |||
ZNF429 | ENST00000597078.5 | c.4-3303A>G | intron_variant | Intron 1 of 5 | 1 | ENSP00000470300.1 | ||||
ZNF429 | ENST00000594022.1 | n.193-2729A>G | intron_variant | Intron 2 of 5 | 3 | |||||
ZNF429 | ENST00000596126.1 | n.469-2729A>G | intron_variant | Intron 1 of 1 | 4 |
Frequencies
GnomAD3 genomes AF: 0.186 AC: 28228AN: 151782Hom.: 2638 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.186 AC: 28236AN: 151900Hom.: 2639 Cov.: 32 AF XY: 0.186 AC XY: 13787AN XY: 74210
GnomAD4 genome
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28236
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151900
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32
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13787
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74210
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Asia WGS
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441
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3478
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