Genetic Variant ZXDB:p.Gly86_Gly89del (chrX-57592292-AGCGGCGGCGGCG-A) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_007157.4(ZXDB):c.257_268delGCGGCGGCGGCG(p.Gly86_Gly89del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000484 in 1,072,555 control chromosomes in the GnomAD database, including 6 homozygotes. There are 233 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00033 ( 0 hom., 5 hem., cov: 23)

Exomes 𝑓: 0.00048 ( 6 hom. 233 hem. )

Failed GnomAD Quality Control

Consequence

ZXDB
NM_007157.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.22

Variant links:

Genes affected

ZXDB (HGNC:13199): (zinc finger X-linked duplicated B) The ZXDB gene is one of a pair of duplicated zinc finger genes on chromosome Xp11.21 (Greig et al., 1993 [PubMed 8268913]); see also ZXDA (MIM 300235).[supplied by OMIM, Jul 2010]

ZXDB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant X-57592292-AGCGGCGGCGGCG-A is Benign according to our data. Variant chrX-57592292-AGCGGCGGCGGCG-A is described in ClinVar as [Likely_benign]. Clinvar id is 2660725.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZXDB	NM_007157.4 link	c.257_268delGCGGCGGCGGCG	p.Gly86_Gly89del	disruptive_inframe_deletion	Exon 1 of 1	ENST00000374888.3	NP_009088.1	P98169

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZXDB	ENST00000374888.3 link	c.257_268delGCGGCGGCGGCG	p.Gly86_Gly89del	disruptive_inframe_deletion	Exon 1 of 1	6	NM_007157.4	ENSP00000364023.1		P98169

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

110495

Hom.:

Cov.:

AF XY:

0.000120

AC XY:

AN XY:

33303

FAILED QC

Gnomad AFR

AF:

0.000131

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000188

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00176

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000170

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000363

Gnomad OTH

AF:

0.00200

GnomAD3 exomes

AF:

0.0000780

AC:

AN:

128269

Hom.:

AF XY:

0.00

AC XY:

AN XY:

41209

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000852

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000420

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000547

Gnomad OTH exome

AF:

0.000315

GnomAD4 exome

AF:

0.000484

AC:

519

AN:

1072555

Hom.:

AF XY:

0.000665

AC XY:

233

AN XY:

350351

show subpopulations

Gnomad4 AFR exome

AF:

0.000331

Gnomad4 AMR exome

AF:

0.000852

Gnomad4 ASJ exome

AF:

0.00252

Gnomad4 EAS exome

AF:

0.00127

Gnomad4 SAS exome

AF:

0.000403

Gnomad4 FIN exome

AF:

0.000119

Gnomad4 NFE exome

AF:

0.000384

Gnomad4 OTH exome

AF:

0.00120

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000326

AC:

AN:

110538

Hom.:

Cov.:

AF XY:

0.000150

AC XY:

AN XY:

33358

show subpopulations

Gnomad4 AFR

AF:

0.000164

Gnomad4 AMR

AF:

0.000188

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00177

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000170

Gnomad4 NFE

AF:

0.000363

Gnomad4 OTH

AF:

0.00198

Alfa

AF:

0.0000367

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ZXDB: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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