rs1814170
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020119.4(ZC3HAV1):c.-72T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,456,612 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000015 ( 0 hom. )
Consequence
ZC3HAV1
NM_020119.4 5_prime_UTR
NM_020119.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.03
Genes affected
ZC3HAV1 (HGNC:23721): (zinc finger CCCH-type containing, antiviral 1) This gene encodes a CCCH-type zinc finger protein. This antiviral protein inhibits viral replication by recruiting cellular RNA degradation machineries to degrade viral mRNAs. The encoded protein plays an important role in the innate immune response against multiple DNA and RNA viruses, including Ebola virus, HIV and SARS-CoV-2 (which causes COVID-19). [provided by RefSeq, Sep 2021]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZC3HAV1 | NM_020119.4 | c.-72T>G | 5_prime_UTR_variant | 1/13 | ENST00000242351.10 | ||
ZC3HAV1 | NM_001363491.2 | c.-72T>G | 5_prime_UTR_variant | 1/13 | |||
ZC3HAV1 | NM_024625.4 | c.-72T>G | 5_prime_UTR_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3HAV1 | ENST00000242351.10 | c.-72T>G | 5_prime_UTR_variant | 1/13 | 1 | NM_020119.4 | A2 | ||
ZC3HAV1 | ENST00000471652.1 | c.-72T>G | 5_prime_UTR_variant | 1/9 | 1 | ||||
ZC3HAV1 | ENST00000680309.1 | c.-127-19644T>G | intron_variant | ||||||
ZC3HAV1 | ENST00000464606.5 | upstream_gene_variant | 5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151994Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000153 AC: 2AN: 1304618Hom.: 0 Cov.: 30 AF XY: 0.00000158 AC XY: 1AN XY: 634784
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GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151994Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74244
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
Cadd
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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