rs17689437
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001305203.2(ZFP90):c.*1750C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 985,408 control chromosomes in the GnomAD database, including 10,319 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 0.13 ( 1435 hom., cov: 32)
Exomes 𝑓: 0.14 ( 8884 hom. )
Consequence
ZFP90
NM_001305203.2 3_prime_UTR
NM_001305203.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0650
Genes affected
ZFP90 (HGNC:23329): (ZFP90 zinc finger protein) This gene encodes a member of the zinc finger protein family that modulates gene expression. The encoded protein derepresses the transcription of certain fetal cardiac genes and may contribute to the genetic reprogramming that occurs during the development of heart failure. Genome wide association studies have identified this gene among ulcerative colitis risk loci. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Mar 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=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZFP90 | NM_001305203.2 | c.*1750C>T | 3_prime_UTR_variant | 5/5 | ENST00000563169.7 | NP_001292132.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZFP90 | ENST00000563169.7 | c.*1750C>T | 3_prime_UTR_variant | 5/5 | 1 | NM_001305203.2 | ENSP00000454418 | P1 |
Frequencies
GnomAD3 genomes AF: 0.131 AC: 19920AN: 152042Hom.: 1435 Cov.: 32
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GnomAD4 exome AF: 0.144 AC: 120195AN: 833246Hom.: 8884 Cov.: 36 AF XY: 0.144 AC XY: 55566AN XY: 384790
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GnomAD4 genome AF: 0.131 AC: 19924AN: 152162Hom.: 1435 Cov.: 32 AF XY: 0.130 AC XY: 9635AN XY: 74384
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at