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GeneBe

7-139076342-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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.24
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.24 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZC3HAV1NM_020119.4 linkuse as main transcriptc.1641G>A p.Thr547= synonymous_variant 6/13 ENST00000242351.10
ZC3HAV1NM_001363491.2 linkuse as main transcriptc.2007G>A p.Thr669= synonymous_variant 6/13
ZC3HAV1NM_024625.4 linkuse as main transcriptc.1641G>A p.Thr547= synonymous_variant 6/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZC3HAV1ENST00000242351.10 linkuse as main transcriptc.1641G>A p.Thr547= synonymous_variant 6/131 NM_020119.4 A2Q7Z2W4-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00688
AC:
1046
AN:
152096
Hom.:
3
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00164
Gnomad AMI
AF:
0.0154
Gnomad AMR
AF:
0.00714
Gnomad ASJ
AF:
0.0288
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00373
Gnomad FIN
AF:
0.00528
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00960
Gnomad OTH
AF:
0.0120
GnomAD3 exomes
AF:
0.00786
AC:
1976
AN:
251482
Hom.:
16
AF XY:
0.00823
AC XY:
1119
AN XY:
135912
show subpopulations
Gnomad AFR exome
AF:
0.00117
Gnomad AMR exome
AF:
0.00442
Gnomad ASJ exome
AF:
0.0328
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00291
Gnomad FIN exome
AF:
0.00485
Gnomad NFE exome
AF:
0.0106
Gnomad OTH exome
AF:
0.0109
GnomAD4 exome
AF:
0.00865
AC:
12647
AN:
1461870
Hom.:
74
Cov.:
31
AF XY:
0.00854
AC XY:
6209
AN XY:
727238
show subpopulations
Gnomad4 AFR exome
AF:
0.00137
Gnomad4 AMR exome
AF:
0.00456
Gnomad4 ASJ exome
AF:
0.0291
Gnomad4 EAS exome
AF:
0.000126
Gnomad4 SAS exome
AF:
0.00296
Gnomad4 FIN exome
AF:
0.00479
Gnomad4 NFE exome
AF:
0.00945
Gnomad4 OTH exome
AF:
0.00878
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00686
AC:
1044
AN:
152214
Hom.:
3
Cov.:
32
AF XY:
0.00672
AC XY:
500
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.00164
Gnomad4 AMR
AF:
0.00713
Gnomad4 ASJ
AF:
0.0288
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00373
Gnomad4 FIN
AF:
0.00528
Gnomad4 NFE
AF:
0.00959
Gnomad4 OTH
AF:
0.0114
Alfa
AF:
0.00998
Hom.:
3
Bravo
AF:
0.00740
Asia WGS
AF:
0.00202
AC:
8
AN:
3478
EpiCase
AF:
0.0116
EpiControl
AF:
0.0132

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 submitterclinical testingInvitaeFeb 02, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
Cadd
Benign
5.3
Dann
Benign
0.77

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs116955781; hg19: chr7-138761088; COSMIC: COSV54295873; API