rs12460279
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_198535.3(ZNF699):c.175+1700T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 152,076 control chromosomes in the GnomAD database, including 17,628 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 0.46 ( 17628 hom., cov: 32)
Consequence
ZNF699
NM_198535.3 intron
NM_198535.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.26
Genes affected
ZNF699 (HGNC:24750): (zinc finger protein 699) 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=-0.57).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF699 | NM_198535.3 | c.175+1700T>C | intron_variant | ENST00000591998.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF699 | ENST00000591998.6 | c.175+1700T>C | intron_variant | 5 | NM_198535.3 | P1 | |||
ZNF699 | ENST00000308650.4 | c.175+1700T>C | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.459 AC: 69735AN: 151958Hom.: 17630 Cov.: 32
GnomAD3 genomes
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69735
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151958
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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: 0.459 AC: 69743AN: 152076Hom.: 17628 Cov.: 32 AF XY: 0.456 AC XY: 33920AN XY: 74316
GnomAD4 genome
?
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AC:
69743
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152076
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32
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33920
AN XY:
74316
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1697
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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