Genetic Variant ZNF711:c.-461_-450dupGGCGGCGGCGGC (chrX-85244123-A-AGGCGGCGGCGGC) – 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.-461_-450dupGGCGGCGGCGGC 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 INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00026 ( 0 hom., 5 hem., cov: 20)

Exomes 𝑓: 0.00023 ( 0 hom. 4 hem. )

Consequence

ZNF711
NM_001330574.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

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 -4 ACMG points.

BS2

High Hemizygotes in GnomAd4 at 5 XL gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330574.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF711	NM_001330574.2	MANE Select	c.-461_-450dupGGCGGCGGCGGC	5_prime_UTR	Exon 1 of 11	NP_001317503.1	Q9Y462-3
ZNF711	NM_001375431.1		c.-82_-71dupGGCGGCGGCGGC	5_prime_UTR	Exon 1 of 9	NP_001362360.1	Q9Y462-3
ZNF711	NM_001375432.1		c.-456_-445dupGGCGGCGGCGGC	5_prime_UTR	Exon 1 of 11	NP_001362361.1	Q9Y462-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF711	ENST00000674551.1	MANE Select	c.-461_-450dupGGCGGCGGCGGC	5_prime_UTR	Exon 1 of 11	ENSP00000502839.1	Q9Y462-3
ZNF711	ENST00000276123.7	TSL:1	c.-456_-445dupGGCGGCGGCGGC	5_prime_UTR	Exon 1 of 10	ENSP00000276123.3	Q9Y462-1
ZNF711	ENST00000373165.7	TSL:1	c.-202_-191dupGGCGGCGGCGGC	5_prime_UTR	Exon 1 of 9	ENSP00000362260.3	Q9Y462-1

Frequencies

GnomAD3 genomes

AF:

0.000258

AC:

AN:

108387

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000307

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000962

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00118

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000230

Gnomad OTH

AF:

0.00138

GnomAD4 exome

AF:

0.000231

AC:

AN:

38904

Hom.:

Cov.:

AF XY:

0.000235

AC XY:

AN XY:

17056

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

686

American (AMR)

AF:

0.00

AC:

AN:

917

Ashkenazi Jewish (ASJ)

AF:

0.00

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:

0.000217

AC:

AN:

27703

Other (OTH)

AF:

0.000924

AC:

AN:

2164

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.000258

AC:

AN:

108416

Hom.:

Cov.:

AF XY:

0.000159

AC XY:

AN XY:

31514

show subpopulations

African (AFR)

AF:

0.000306

AC:

AN:

29401

American (AMR)

AF:

0.0000961

AC:

AN:

10406

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2613

East Asian (EAS)

AF:

0.00118

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:

0.00

AC:

AN:

213

European-Non Finnish (NFE)

AF:

0.000231

AC:

AN:

52060

Other (OTH)

AF:

0.00136

AC:

AN:

1471

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.447

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000112

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.93

Mutation Taster

=299/1

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over