rs931608
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000593802.1(ZNF98):c.316-27808T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 151,942 control chromosomes in the GnomAD database, including 55,606 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 0.85 ( 55606 hom., cov: 31)
Consequence
ZNF98
ENST00000593802.1 intron
ENST00000593802.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.14
Genes affected
ZNF98 (HGNC:13174): (zinc finger protein 98) 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]
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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=-1.01).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF98 | ENST00000593802.1 | c.316-27808T>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.854 AC: 129728AN: 151824Hom.: 55575 Cov.: 31
GnomAD3 genomes
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151824
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.854 AC: 129813AN: 151942Hom.: 55606 Cov.: 31 AF XY: 0.852 AC XY: 63239AN XY: 74222
GnomAD4 genome
?
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AC:
129813
AN:
151942
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Cov.:
31
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63239
AN XY:
74222
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Asia WGS
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3009
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at