chr7-139076342-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_020119.4(ZC3HAV1):c.1641G>A(p.Thr547=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00848 in 1,614,084 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0069 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0087 ( 74 hom. )
Consequence
ZC3HAV1
NM_020119.4 synonymous
NM_020119.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.24
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 Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
Variant 7-139076342-C-T is Benign according to our data. Variant chr7-139076342-C-T is described in ClinVar as [Benign]. Clinvar id is 788271.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.24 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZC3HAV1 | NM_020119.4 | c.1641G>A | p.Thr547= | synonymous_variant | 6/13 | ENST00000242351.10 | |
ZC3HAV1 | NM_001363491.2 | c.2007G>A | p.Thr669= | synonymous_variant | 6/13 | ||
ZC3HAV1 | NM_024625.4 | c.1641G>A | p.Thr547= | synonymous_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3HAV1 | ENST00000242351.10 | c.1641G>A | p.Thr547= | synonymous_variant | 6/13 | 1 | NM_020119.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00688 AC: 1046AN: 152096Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00786 AC: 1976AN: 251482Hom.: 16 AF XY: 0.00823 AC XY: 1119AN XY: 135912
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GnomAD4 exome AF: 0.00865 AC: 12647AN: 1461870Hom.: 74 Cov.: 31 AF XY: 0.00854 AC XY: 6209AN XY: 727238
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GnomAD4 genome ? AF: 0.00686 AC: 1044AN: 152214Hom.: 3 Cov.: 32 AF XY: 0.00672 AC XY: 500AN XY: 74420
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 02, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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