X-47846275-C-T

Position:

chrX-47846275-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_007137.5(ZNF81):c.8C>T(p.Ala3Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0161 in 1,207,460 control chromosomes in the GnomAD database, including 136 homozygotes. There are 6,115 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.012 ( 13 hom., 344 hem., cov: 23)

Exomes 𝑓: 0.017 ( 123 hom. 5771 hem. )

Consequence

ZNF81
NM_007137.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.245

Variant links:

Genes affected

ZNF81 (HGNC:13156): (zinc finger protein 81) This gene encodes a protein that likely functions as a transcription factor. The protein contains an N-terminal KRAB domain and several C2H2-type zinc finger motifs. Mutations in this gene cause an X-linked form of intellectual disability (MRX45). Microduplication of a region of chromosome X including this gene has also been associated with other forms of intellectual disability. [provided by RefSeq, Jul 2017]

ZNF81 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0035823584).

BP6

Variant X-47846275-C-T is Benign according to our data. Variant chrX-47846275-C-T is described in ClinVar as [Benign]. Clinvar id is 130859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-47846275-C-T is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0117 (1309/112342) while in subpopulation NFE AF= 0.0187 (997/53230). AF 95% confidence interval is 0.0178. There are 13 homozygotes in gnomad4. There are 344 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 13 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF81	NM_007137.5 linkuse as main transcript	c.8C>T	p.Ala3Val	missense_variant	2/5	ENST00000338637.13	NP_009068.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF81	ENST00000338637.13 linkuse as main transcript	c.8C>T	p.Ala3Val	missense_variant	2/5	3	NM_007137.5	ENSP00000341151	P1

Frequencies

GnomAD3 genomes

AF:

0.0117

AC:

1313

AN:

112290

Hom.:

Cov.:

AF XY:

0.00999

AC XY:

344

AN XY:

34440

show subpopulations

Gnomad AFR

AF:

0.00305

Gnomad AMI

AF:

0.0425

Gnomad AMR

AF:

0.0124

Gnomad ASJ

AF:

0.00604

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00110

Gnomad FIN

AF:

0.00323

Gnomad MID

AF:

0.0210

Gnomad NFE

AF:

0.0187

Gnomad OTH

AF:

0.0112

GnomAD3 exomes

AF:

0.00925

AC:

1607

AN:

173816

Hom.:

AF XY:

0.00854

AC XY:

519

AN XY:

60784

show subpopulations

Gnomad AFR exome

AF:

0.00286

Gnomad AMR exome

AF:

0.00574

Gnomad ASJ exome

AF:

0.00589

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00130

Gnomad FIN exome

AF:

0.00294

Gnomad NFE exome

AF:

0.0163

Gnomad OTH exome

AF:

0.0103

GnomAD4 exome

AF:

0.0166

AC:

18178

AN:

1095118

Hom.:

123

Cov.:

AF XY:

0.0160

AC XY:

5771

AN XY:

361160

show subpopulations

Gnomad4 AFR exome

AF:

0.00239

Gnomad4 AMR exome

AF:

0.00614

Gnomad4 ASJ exome

AF:

0.00574

Gnomad4 EAS exome

AF:

0.0000332

Gnomad4 SAS exome

AF:

0.00158

Gnomad4 FIN exome

AF:

0.00343

Gnomad4 NFE exome

AF:

0.0201

Gnomad4 OTH exome

AF:

0.0138

GnomAD4 genome

AF:

0.0117

AC:

1309

AN:

112342

Hom.:

Cov.:

AF XY:

0.00997

AC XY:

344

AN XY:

34502

show subpopulations

Gnomad4 AFR

AF:

0.00304

Gnomad4 AMR

AF:

0.0124

Gnomad4 ASJ

AF:

0.00604

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00110

Gnomad4 FIN

AF:

0.00323

Gnomad4 NFE

AF:

0.0187

Gnomad4 OTH

AF:

0.0111

Alfa

AF:

0.0153

Hom.:

644

Bravo

AF:

0.0120

TwinsUK

AF:

0.0183

AC:

ALSPAC

AF:

0.0208

AC:

ESP6500AA

AF:

0.00260

AC:

ESP6500EA

AF:

0.0200

AC:

130

ExAC

AF:

0.00894

AC:

1081

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Dec 27, 2012

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

History of neurodevelopmental disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 20, 2012

This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.043

T;T;.;.

FATHMM_MKL

Benign

0.083

LIST_S2

Benign

0.52

.;T;T;T

MetaRNN

Benign

0.0036

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.7

L;L;.;.

MutationTaster

Benign

1.0

N;N;N

PrimateAI

Benign

0.35

PROVEAN

Benign

-0.030

N;N;N;N

REVEL

Benign

0.027

Sift

Uncertain

0.0060

D;D;T;T

Sift4G

Uncertain

0.036

D;D;T;T

Polyphen

0.32

B;B;.;.

Vest4

0.073

MVP

0.44

MPC

0.15

ClinPred

0.0037

GERP RS

2.7

Varity_R

0.11

gMVP

0.15

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over