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:

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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

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X-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