Variant chr15-90067682-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_198526.4(ZNF710):c.545T>G(p.Leu182Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00688 in 1,612,710 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0057 ( 11 hom., cov: 32)

Exomes 𝑓: 0.0070 ( 46 hom. )

Consequence

ZNF710
NM_198526.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.155

Variant links:

Genes affected

ZNF710 (HGNC:25352): (zinc finger protein 710) Predicted to enable DNA-binding transcription factor activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF710 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0039324164).

BP6

Variant 15-90067682-T-G is Benign according to our data. Variant chr15-90067682-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 2645702.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 867 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF710	NM_198526.4 linkuse as main transcript	c.545T>G	p.Leu182Arg	missense_variant	2/5	ENST00000268154.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF710	ENST00000268154.9 linkuse as main transcript	c.545T>G	p.Leu182Arg	missense_variant	2/5	2	NM_198526.4	P1

Frequencies

GnomAD3 genomes

AF:

0.00571

AC:

868

AN:

152134

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000820

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00137

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.0113

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00991

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00562

AC:

1363

AN:

242462

Hom.:

AF XY:

0.00555

AC XY:

736

AN XY:

132544

show subpopulations

Gnomad AFR exome

AF:

0.000881

Gnomad AMR exome

AF:

0.00175

Gnomad ASJ exome

AF:

0.00112

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000296

Gnomad FIN exome

AF:

0.0128

Gnomad NFE exome

AF:

0.00889

Gnomad OTH exome

AF:

0.00641

GnomAD4 exome

AF:

0.00700

AC:

10229

AN:

1460458

Hom.:

Cov.:

AF XY:

0.00711

AC XY:

5168

AN XY:

726556

show subpopulations

Gnomad4 AFR exome

AF:

0.000807

Gnomad4 AMR exome

AF:

0.00175

Gnomad4 ASJ exome

AF:

0.00123

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.000418

Gnomad4 FIN exome

AF:

0.0122

Gnomad4 NFE exome

AF:

0.00821

Gnomad4 OTH exome

AF:

0.00469

GnomAD4 genome

AF:

0.00569

AC:

867

AN:

152252

Hom.:

Cov.:

AF XY:

0.00531

AC XY:

395

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.000818

Gnomad4 AMR

AF:

0.00137

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.0113

Gnomad4 NFE

AF:

0.00990

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00780

Hom.:

Bravo

AF:

0.00414

TwinsUK

AF:

0.00270

AC:

ALSPAC

AF:

0.00493

AC:

ESP6500AA

AF:

0.00139

AC:

ESP6500EA

AF:

0.00656

AC:

ExAC

AF:

0.00550

AC:

664

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00731

EpiControl

AF:

0.00670

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

ZNF710: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.081

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.030

Eigen

Benign

-0.60

Eigen_PC

Benign

-0.49

FATHMM_MKL

Benign

0.36

LIST_S2

Benign

0.67

MetaRNN

Benign

0.0039

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.81

MutationTaster

Benign

0.77

PrimateAI

Uncertain

0.74

PROVEAN

Benign

-0.55

REVEL

Benign

0.16

Sift

Benign

0.039

Sift4G

Benign

0.34

Polyphen

0.0020

Vest4

0.31

MVP

0.18

MPC

1.2

ClinPred

0.017

GERP RS

5.0

Varity_R

0.22

gMVP

0.34

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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