Genetic Variant ZNF711:c.-452_-450dupGGC (chrX-85244123-A-AGGC) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001330574.2(ZNF711):c.-452_-450dupGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0019 ( 0 hom., 45 hem., cov: 20)

Exomes 𝑓: 0.0022 ( 1 hom. 33 hem. )

Consequence

ZNF711
NM_001330574.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.933

Publications

1 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 -6 ACMG points.

BP6

Variant X-85244123-A-AGGC is Benign according to our data. Variant chrX-85244123-A-AGGC is described in ClinVar as [Likely_benign]. Clinvar id is 368738.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 45 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF711	NM_001330574.2 link	c.-452_-450dupGGC		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.-452_-450dupGGC	5_prime_UTR_variant	Exon 1 of 11		NM_001330574.2	ENSP00000502839.1	Q9Y462-3
ZNF711	ENST00000276123.7 link	c.-447_-445dupGGC	5_prime_UTR_variant	Exon 1 of 10	1		ENSP00000276123.3	Q9Y462-1
ZNF711	ENST00000373165.7 link	c.-193_-191dupGGC	5_prime_UTR_variant	Exon 1 of 9	1		ENSP00000362260.3	Q9Y462-1
SATL1	ENST00000646235.1 link	c.-1434_-1432dupGCC	upstream_gene_variant				ENSP00000495329.1	A0A2R8YFQ0

Frequencies

GnomAD3 genomes

AF:

0.00194

AC:

210

AN:

108386

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00187

Gnomad AMI

AF:

0.00149

Gnomad AMR

AF:

0.00183

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00441

Gnomad SAS

AF:

0.00747

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00194

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00224

AC:

AN:

38889

Hom.:

Cov.:

AF XY:

0.00194

AC XY:

AN XY:

17039

show subpopulations

African (AFR)

AF:

0.00147

AC:

AN:

682

American (AMR)

AF:

0.00218

AC:

AN:

917

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

660

East Asian (EAS)

AF:

0.00225

AC:

AN:

2221

South Asian (SAS)

AF:

0.00327

AC:

AN:

1835

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2556

Middle Eastern (MID)

AF:

0.00

AC:

AN:

160

European-Non Finnish (NFE)

AF:

0.00242

AC:

AN:

27692

Other (OTH)

AF:

0.00277

AC:

AN:

2166

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00193

AC:

209

AN:

108415

Hom.:

Cov.:

AF XY:

0.00143

AC XY:

AN XY:

31513

show subpopulations

African (AFR)

AF:

0.00187

AC:

AN:

29403

American (AMR)

AF:

0.00183

AC:

AN:

10407

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2613

East Asian (EAS)

AF:

0.00414

AC:

AN:

3385

South Asian (SAS)

AF:

0.00750

AC:

AN:

2534

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5660

Middle Eastern (MID)

AF:

0.00

AC:

AN:

213

European-Non Finnish (NFE)

AF:

0.00194

AC:

101

AN:

52056

Other (OTH)

AF:

0.00

AC:

AN:

1471

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Non-syndromic X-linked intellectual disability

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.93

Mutation Taster

=300/0

polymorphism

(source)

Splicing

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

Publications

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chrX-85244123-A-AGGC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over