Genetic Variant ZNF711:c.-458_-438delGGCGGCGGCAGCGGCGGCGGC (chrX-85244127-GGCGGCGGCGGCGGCGGCGGCA-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001330574.2(ZNF711):c.-458_-438delGGCGGCGGCAGCGGCGGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00025 ( 0 hom., 3 hem., cov: 20)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

ZNF711
NM_001330574.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.75

Publications

0 publications found

Variant links:

Genes affected

ZNF711 (HGNC:13128): (zinc finger protein 711) This gene encodes a zinc finger protein of unknown function. It bears similarity to a zinc finger protein which acts as a transcriptional activator. This gene lies in a region of the X chromosome which has been associated with cognitive disability. [provided by RefSeq, Jul 2008]

ZNF711 links:

SATL1 (HGNC:27992): (spermidine/spermine N1-acetyl transferase like 1) Predicted to enable N-acetyltransferase activity. [provided by Alliance of Genome Resources, Apr 2022]

SATL1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Hemizygotes in GnomAd4 at 3 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF711	NM_001330574.2 link	c.-458_-438delGGCGGCGGCAGCGGCGGCGGC		5_prime_UTR_variant	Exon 1 of 11	ENST00000674551.1	NP_001317503.1	Q9Y462-3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZNF711	ENST00000674551.1 link	c.-458_-438delGGCGGCGGCAGCGGCGGCGGC	5_prime_UTR_variant	Exon 1 of 11		NM_001330574.2	ENSP00000502839.1	Q9Y462-3
ZNF711	ENST00000276123.7 link	c.-453_-433delGGCGGCGGCAGCGGCGGCGGC	5_prime_UTR_variant	Exon 1 of 10	1		ENSP00000276123.3	Q9Y462-1
ZNF711	ENST00000373165.7 link	c.-199_-179delGGCGGCGGCAGCGGCGGCGGC	5_prime_UTR_variant	Exon 1 of 9	1		ENSP00000362260.3	Q9Y462-1
SATL1	ENST00000646235.1 link	c.-1456_-1436delTGCCGCCGCCGCCGCCGCCGC	upstream_gene_variant				ENSP00000495329.1	A0A2R8YFQ0

Frequencies

GnomAD3 genomes

AF:

0.000248

AC:

AN:

108989

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000335

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000290

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000290

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000422

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

38643

Hom.:

AF XY:

0.00

AC XY:

AN XY:

16731

African (AFR)

AF:

0.00

AC:

AN:

719

American (AMR)

AF:

0.00

AC:

AN:

905

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

618

East Asian (EAS)

AF:

0.00

AC:

AN:

2232

South Asian (SAS)

AF:

0.00

AC:

AN:

1785

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2516

Middle Eastern (MID)

AF:

0.00

AC:

AN:

163

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

27547

Other (OTH)

AF:

0.00

AC:

AN:

2158

GnomAD4 genome

AF:

0.000248

AC:

AN:

109025

Hom.:

Cov.:

AF XY:

0.0000938

AC XY:

AN XY:

31991

show subpopulations

African (AFR)

AF:

0.0000334

AC:

AN:

29934

American (AMR)

AF:

0.000289

AC:

AN:

10364

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2559

East Asian (EAS)

AF:

0.000291

AC:

AN:

3434

South Asian (SAS)

AF:

0.00

AC:

AN:

2545

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5657

Middle Eastern (MID)

AF:

0.00

AC:

AN:

213

European-Non Finnish (NFE)

AF:

0.000422

AC:

AN:

52169

Other (OTH)

AF:

0.00

AC:

AN:

1480

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.000295

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Intellectual disability, X-linked 97

Uncertain:1

Feb 18, 2022

Revvity Omics, Revvity

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.8

Mutation Taster

=297/3

polymorphism

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

chrX-85244127-GGCGGCGGCGGCGGCGGCGGCA-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over