Genetic Variant ZC3H7B:p.Asp72Asp (chr22-41325849-C-T) – ACMG Classification: Benign (-13 pts)

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

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]

ZC3H7B links:

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
ZC3H7B	NM_017590.6 link	c.216C>T	p.Asp72Asp	synonymous_variant	Exon 4 of 23	ENST00000352645.5	NP_060060.3	Q9UGR2
ZC3H7B	XR_007067960.1 link	n.470C>T		non_coding_transcript_exon_variant	Exon 4 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZC3H7B	ENST00000352645.5 link	c.216C>T	p.Asp72Asp	synonymous_variant	Exon 4 of 23	1	NM_017590.6	ENSP00000345793.4		Q9UGR2
ZC3H7B	ENST00000486331.1 link	n.280C>T		non_coding_transcript_exon_variant	Exon 4 of 7	2

Frequencies

GnomAD3 genomes

AF:

0.00424

AC:

645

AN:

152230

Hom.:

Cov.:

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.:

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.:

Cov.:

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.:

Cov.:

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.:

Bravo

AF:

0.00390

Asia WGS

AF:

0.00173

AC:

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

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over