rs16964544
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001376110.1(ZNF536):c.3896-16325A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,938 control chromosomes in the GnomAD database, including 10,253 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 0.36 ( 10253 hom., cov: 32)
Consequence
ZNF536
NM_001376110.1 intron
NM_001376110.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.223
Genes affected
ZNF536 (HGNC:29025): (zinc finger protein 536) The protein encoded by this gene is a highly conserved zinc finger protein. The encoded protein is most abundant in brain, where it negatively regulates neuronal differentiation. [provided by RefSeq, Sep 2015]
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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=-0.98).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF536 | NM_001352260.2 | c.*27-16325A>G | intron_variant | ||||
ZNF536 | NM_001376110.1 | c.3896-16325A>G | intron_variant | ||||
ZNF536 | NM_001376111.1 | c.3896-16325A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF536 | ENST00000592773.3 | c.3896-16325A>G | intron_variant | 5 | P1 | ||||
ZNF536 | ENST00000706143.1 | c.1649-16325A>G | intron_variant | ||||||
ZNF536 | ENST00000706147.1 | c.2324-16325A>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.359 AC: 54560AN: 151820Hom.: 10241 Cov.: 32
GnomAD3 genomes
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151820
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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: 0.360 AC: 54622AN: 151938Hom.: 10253 Cov.: 32 AF XY: 0.361 AC XY: 26772AN XY: 74256
GnomAD4 genome
?
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54622
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151938
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32
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26772
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74256
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1584
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at