rs9638416
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015852.5(ZNF117):c.*2391A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.949 in 152,178 control chromosomes in the GnomAD database, including 68,965 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 0.95 ( 68965 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
ZNF117
NM_015852.5 3_prime_UTR
NM_015852.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.981
Genes affected
ZNF117 (HGNC:12897): (zinc finger protein 117) This gene encodes a protein containing multiple C2H2-type zinc finger motifs. Readthrough transcription occurs between this gene and the upstream endogenous retrovirus group 3 member 1 (ERV3-1) locus, and may result in additional transcript variants encoding the zinc finger protein. [provided by RefSeq, Jan 2017]
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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 = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF117 | NM_015852.5 | c.*2391A>G | 3_prime_UTR_variant | 4/4 | ENST00000282869.11 | ||
ERV3-1-ZNF117 | NM_001348050.2 | c.*2391A>G | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF117 | ENST00000282869.11 | c.*2391A>G | 3_prime_UTR_variant | 4/4 | 1 | NM_015852.5 | P1 | ||
ZNF117 | ENST00000620222.4 | c.*2391A>G | 3_prime_UTR_variant | 3/3 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.949 AC: 144296AN: 152060Hom.: 68938 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
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GnomAD4 genome ? AF: 0.949 AC: 144375AN: 152178Hom.: 68965 Cov.: 32 AF XY: 0.950 AC XY: 70665AN XY: 74408
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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