Variant 15-90067578-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_198526.4(ZNF710):c.441C>T(p.Cys147=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000824 in 1,609,652 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00079 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00083 ( 2 hom. )

Consequence

ZNF710
NM_198526.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.09

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 15-90067578-C-T is Benign according to our data. Variant chr15-90067578-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2645701.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-3.09 with no splicing effect.

BS2

High AC in GnomAd4 at 121 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF710	NM_198526.4 linkuse as main transcript	c.441C>T	p.Cys147=	synonymous_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.441C>T	p.Cys147=	synonymous_variant	2/5	2	NM_198526.4	P1

Frequencies

GnomAD3 genomes

AF:

0.000795

AC:

121

AN:

152238

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000217

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000981

Gnomad ASJ

AF:

0.0112

Gnomad EAS

AF:

0.000961

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.000470

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000617

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00121

AC:

283

AN:

233922

Hom.:

AF XY:

0.00128

AC XY:

164

AN XY:

127912

show subpopulations

Gnomad AFR exome

AF:

0.000279

Gnomad AMR exome

AF:

0.000421

Gnomad ASJ exome

AF:

0.0131

Gnomad EAS exome

AF:

0.000230

Gnomad SAS exome

AF:

0.000605

Gnomad FIN exome

AF:

0.000606

Gnomad NFE exome

AF:

0.000885

Gnomad OTH exome

AF:

0.00210

GnomAD4 exome

AF:

0.000827

AC:

1205

AN:

1457296

Hom.:

Cov.:

AF XY:

0.000844

AC XY:

612

AN XY:

724722

show subpopulations

Gnomad4 AFR exome

AF:

0.000329

Gnomad4 AMR exome

AF:

0.000591

Gnomad4 ASJ exome

AF:

0.0116

Gnomad4 EAS exome

AF:

0.000127

Gnomad4 SAS exome

AF:

0.000677

Gnomad4 FIN exome

AF:

0.000322

Gnomad4 NFE exome

AF:

0.000632

Gnomad4 OTH exome

AF:

0.00117

GnomAD4 genome

AF:

0.000794

AC:

121

AN:

152356

Hom.:

Cov.:

AF XY:

0.000819

AC XY:

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.000216

Gnomad4 AMR

AF:

0.000980

Gnomad4 ASJ

AF:

0.0112

Gnomad4 EAS

AF:

0.000963

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.000470

Gnomad4 NFE

AF:

0.000618

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00149

Hom.:

Bravo

AF:

0.000858

Asia WGS

AF:

0.000866

AC:

AN:

3478

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: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

1.4

DANN

Benign

0.68

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