Variant 19-11948652-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_144566.3(ZNF700):c.628C>G(p.Arg210Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0376 in 1,611,612 control chromosomes in the GnomAD database, including 1,609 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.063 ( 471 hom., cov: 33)

Exomes 𝑓: 0.035 ( 1138 hom. )

Consequence

ZNF700
NM_144566.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.24

Variant links:

Genes affected

ZNF700 (HGNC:25292): (zinc finger protein 700) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF700 links:

ENSG00000267179 (HGNC:):

ENSG00000267179 links:

ZNF69 (HGNC:13138): (zinc finger protein 69) Enables identical protein binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF69 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0018607676).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF700	NM_144566.3 linkuse as main transcript	c.628C>G	p.Arg210Gly	missense_variant	4/4	ENST00000254321.10	NP_653167.1	Q9H0M5
ZNF700	NM_001271848.2 linkuse as main transcript	c.637C>G	p.Arg213Gly	missense_variant	4/4		NP_001258777.1	Q9H0M5A0A087WVH9
ZNF69	XM_017027231.2 linkuse as main transcript	c.500-31389C>G		intron_variant			XP_016882720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF700	ENST00000254321.10 linkuse as main transcript	c.628C>G	p.Arg210Gly	missense_variant	4/4	1	NM_144566.3	ENSP00000254321.4		Q9H0M5
ENSG00000267179	ENST00000590798.1 linkuse as main transcript	c.63+23379C>G		intron_variant		2		ENSP00000467286.1		F5H0A9

Frequencies

GnomAD3 genomes

AF:

0.0632

AC:

9610

AN:

152046

Hom.:

469

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.0417

Gnomad ASJ

AF:

0.0216

Gnomad EAS

AF:

0.0221

Gnomad SAS

AF:

0.0406

Gnomad FIN

AF:

0.0615

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0315

Gnomad OTH

AF:

0.0593

GnomAD3 exomes

AF:

0.0405

AC:

10077

AN:

248938

Hom.:

328

AF XY:

0.0394

AC XY:

5310

AN XY:

134624

show subpopulations

Gnomad AFR exome

AF:

0.136

Gnomad AMR exome

AF:

0.0247

Gnomad ASJ exome

AF:

0.0211

Gnomad EAS exome

AF:

0.0259

Gnomad SAS exome

AF:

0.0405

Gnomad FIN exome

AF:

0.0569

Gnomad NFE exome

AF:

0.0326

Gnomad OTH exome

AF:

0.0392

GnomAD4 exome

AF:

0.0349

AC:

50948

AN:

1459448

Hom.:

1138

Cov.:

AF XY:

0.0350

AC XY:

25429

AN XY:

726058

show subpopulations

Gnomad4 AFR exome

AF:

0.134

Gnomad4 AMR exome

AF:

0.0272

Gnomad4 ASJ exome

AF:

0.0208

Gnomad4 EAS exome

AF:

0.0257

Gnomad4 SAS exome

AF:

0.0397

Gnomad4 FIN exome

AF:

0.0547

Gnomad4 NFE exome

AF:

0.0313

Gnomad4 OTH exome

AF:

0.0376

GnomAD4 genome

AF:

0.0632

AC:

9616

AN:

152164

Hom.:

471

Cov.:

AF XY:

0.0641

AC XY:

4771

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.136

Gnomad4 AMR

AF:

0.0417

Gnomad4 ASJ

AF:

0.0216

Gnomad4 EAS

AF:

0.0220

Gnomad4 SAS

AF:

0.0406

Gnomad4 FIN

AF:

0.0615

Gnomad4 NFE

AF:

0.0315

Gnomad4 OTH

AF:

0.0587

Alfa

AF:

0.0311

Hom.:

Bravo

AF:

0.0638

TwinsUK

AF:

0.0326

AC:

121

ALSPAC

AF:

0.0358

AC:

138

ESP6500AA

AF:

0.133

AC:

584

ESP6500EA

AF:

0.0298

AC:

256

ExAC

AF:

0.0434

AC:

5272

Asia WGS

AF:

0.0290

AC:

103

AN:

3478

EpiCase

AF:

0.0314

EpiControl

AF:

0.0324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.32

BayesDel_addAF

Benign

-0.72

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.062

T;.;.

Eigen

Benign

-0.58

Eigen_PC

Benign

-0.84

FATHMM_MKL

Benign

0.0

LIST_S2

Benign

0.000087

T;T;T

MetaRNN

Benign

0.0019

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.7

L;.;.

PrimateAI

Benign

0.21

PROVEAN

Uncertain

-3.9

D;.;.

REVEL

Benign

0.042

Sift

Uncertain

0.017

D;.;.

Sift4G

Benign

0.15

T;T;T

Polyphen

0.94

P;.;.

Vest4

0.11

MPC

0.024

ClinPred

0.038

GERP RS

0.55

Varity_R

0.24

gMVP

0.021

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over