Genetic Variant ZNF711:c.-455_-450dupGGCGGC (chrX-85244123-A-AGGCGGC) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001330574.2(ZNF711):c.-455_-450dupGGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.033 ( 175 hom., 714 hem., cov: 20)

Exomes 𝑓: 0.0026 ( 5 hom. 34 hem. )

Consequence

ZNF711
NM_001330574.2 5_prime_UTR

Scores

Not classified

Clinical Significance

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: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF711	NM_001330574.2 link	c.-455_-450dupGGCGGC		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.-455_-450dupGGCGGC	5_prime_UTR_variant	Exon 1 of 11		NM_001330574.2	ENSP00000502839.1	Q9Y462-3
ZNF711	ENST00000276123.7 link	c.-450_-445dupGGCGGC	5_prime_UTR_variant	Exon 1 of 10	1		ENSP00000276123.3	Q9Y462-1
ZNF711	ENST00000373165.7 link	c.-196_-191dupGGCGGC	5_prime_UTR_variant	Exon 1 of 9	1		ENSP00000362260.3	Q9Y462-1
SATL1	ENST00000646235.1 link	c.-1437_-1432dupGCCGCC	upstream_gene_variant				ENSP00000495329.1	A0A2R8YFQ0

Frequencies

GnomAD3 genomes

AF:

0.0328

AC:

3555

AN:

108331

Hom.:

175

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00962

Gnomad ASJ

AF:

0.00230

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00429

Gnomad NFE

AF:

0.000672

Gnomad OTH

AF:

0.0179

GnomAD4 exome

AF:

0.00260

AC:

101

AN:

38898

Hom.:

Cov.:

AF XY:

0.00199

AC XY:

AN XY:

17052

show subpopulations

African (AFR)

AF:

0.0959

AC:

AN:

678

American (AMR)

AF:

0.00218

AC:

AN:

917

Ashkenazi Jewish (ASJ)

AF:

0.00606

AC:

AN:

660

East Asian (EAS)

AF:

0.00

AC:

AN:

2221

South Asian (SAS)

AF:

0.000544

AC:

AN:

1837

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2556

Middle Eastern (MID)

AF:

0.00

AC:

AN:

160

European-Non Finnish (NFE)

AF:

0.000469

AC:

AN:

27705

Other (OTH)

AF:

0.00739

AC:

AN:

2164

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.454

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0328

AC:

3559

AN:

108360

Hom.:

175

Cov.:

AF XY:

0.0227

AC XY:

714

AN XY:

31492

show subpopulations

African (AFR)

AF:

0.116

AC:

3392

AN:

29344

American (AMR)

AF:

0.00951

AC:

AN:

10407

Ashkenazi Jewish (ASJ)

AF:

0.00230

AC:

AN:

2613

East Asian (EAS)

AF:

0.00

AC:

AN:

3385

South Asian (SAS)

AF:

0.00

AC:

AN:

2534

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5660

Middle Eastern (MID)

AF:

0.00469

AC:

AN:

213

European-Non Finnish (NFE)

AF:

0.000672

AC:

AN:

52060

Other (OTH)

AF:

0.0177

AC:

AN:

1471

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

106

212

318

424

530

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Significance: 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: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 (auto)

(source)

Splicing

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

Publications

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X-85244123-AGGCGGCGGCGGCGGC-AGGCGGCGGCGGCGGCGGCGGC

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