22-41325849-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_017590.6(ZC3H7B):​c.216C>T​(p.Asp72Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00478 in 1,612,670 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0048 ( 48 hom. )

Consequence

ZC3H7B
NM_017590.6 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.452
Variant links:
Genes affected
ZC3H7B (HGNC:30869): (zinc finger CCCH-type containing 7B) This gene encodes a protein that contains a tetratricopeptide repeat domain. The encoded protein also interacts with the rotavirus non-structural protein NSP3. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
Variant 22-41325849-C-T is Benign according to our data. Variant chr22-41325849-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2653226.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.452 with no splicing effect.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00484 (7064/1460322) while in subpopulation MID AF= 0.0333 (171/5128). AF 95% confidence interval is 0.0293. There are 48 homozygotes in gnomad4_exome. There are 3559 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 642 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZC3H7BNM_017590.6 linkc.216C>T p.Asp72Asp synonymous_variant Exon 4 of 23 ENST00000352645.5 NP_060060.3 Q9UGR2
ZC3H7BXR_007067960.1 linkn.470C>T non_coding_transcript_exon_variant Exon 4 of 15

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZC3H7BENST00000352645.5 linkc.216C>T p.Asp72Asp synonymous_variant Exon 4 of 23 1 NM_017590.6 ENSP00000345793.4 Q9UGR2
ZC3H7BENST00000486331.1 linkn.280C>T non_coding_transcript_exon_variant Exon 4 of 7 2

Frequencies

GnomAD3 genomes
AF:
0.00424
AC:
645
AN:
152230
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000989
Gnomad AMI
AF:
0.0143
Gnomad AMR
AF:
0.00537
Gnomad ASJ
AF:
0.0104
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00207
Gnomad FIN
AF:
0.00988
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.00488
Gnomad OTH
AF:
0.00860
GnomAD3 exomes
AF:
0.00494
AC:
1232
AN:
249350
Hom.:
10
AF XY:
0.00507
AC XY:
684
AN XY:
134796
show subpopulations
Gnomad AFR exome
AF:
0.000871
Gnomad AMR exome
AF:
0.00440
Gnomad ASJ exome
AF:
0.0112
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00241
Gnomad FIN exome
AF:
0.0104
Gnomad NFE exome
AF:
0.00544
Gnomad OTH exome
AF:
0.00737
GnomAD4 exome
AF:
0.00484
AC:
7064
AN:
1460322
Hom.:
48
Cov.:
32
AF XY:
0.00490
AC XY:
3559
AN XY:
726402
show subpopulations
Gnomad4 AFR exome
AF:
0.00185
Gnomad4 AMR exome
AF:
0.00455
Gnomad4 ASJ exome
AF:
0.0122
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00222
Gnomad4 FIN exome
AF:
0.00822
Gnomad4 NFE exome
AF:
0.00479
Gnomad4 OTH exome
AF:
0.00582
GnomAD4 genome
AF:
0.00421
AC:
642
AN:
152348
Hom.:
4
Cov.:
32
AF XY:
0.00426
AC XY:
317
AN XY:
74496
show subpopulations
Gnomad4 AFR
AF:
0.000986
Gnomad4 AMR
AF:
0.00536
Gnomad4 ASJ
AF:
0.0104
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00186
Gnomad4 FIN
AF:
0.00988
Gnomad4 NFE
AF:
0.00488
Gnomad4 OTH
AF:
0.00851
Alfa
AF:
0.00496
Hom.:
2
Bravo
AF:
0.00390
Asia WGS
AF:
0.00173
AC:
6
AN:
3478
EpiCase
AF:
0.00731
EpiControl
AF:
0.00744

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
May 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

ZC3H7B: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
CADD
Benign
11
DANN
Benign
0.66
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs151077891; hg19: chr22-41721853; API