Variant 20-63960107-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_020713.3(ZNF512B):c.2460C>T(p.Pro820Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0624 in 1,613,860 control chromosomes in the GnomAD database, including 3,655 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.045 ( 251 hom., cov: 33)

Exomes 𝑓: 0.064 ( 3404 hom. )

Consequence

ZNF512B
NM_020713.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.797

Variant links:

Genes affected

ZNF512B (HGNC:29212): (zinc finger protein 512B) Predicted to enable DNA binding activity and metal ion binding activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF512B 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 (BayesDel_noAF=-0.46).

BP6

Variant 20-63960107-G-A is Benign according to our data. Variant chr20-63960107-G-A is described in ClinVar as [Benign]. Clinvar id is 3059327.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.797 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF512B	NM_020713.3 linkuse as main transcript	c.2460C>T	p.Pro820Pro	synonymous_variant	17/17	ENST00000369888.6	NP_065764.1	Q96KM6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF512B	ENST00000369888.6 linkuse as main transcript	c.2460C>T	p.Pro820Pro	synonymous_variant	17/17	1	NM_020713.3	ENSP00000358904.1		Q96KM6

Frequencies

GnomAD3 genomes

AF:

0.0447

AC:

6810

AN:

152214

Hom.:

251

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0116

Gnomad AMI

AF:

0.0846

Gnomad AMR

AF:

0.0266

Gnomad ASJ

AF:

0.0308

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.0269

Gnomad FIN

AF:

0.0522

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0729

Gnomad OTH

AF:

0.0411

GnomAD3 exomes

AF:

0.0456

AC:

11431

AN:

250450

Hom.:

311

AF XY:

0.0471

AC XY:

6395

AN XY:

135690

show subpopulations

Gnomad AFR exome

AF:

0.0118

Gnomad AMR exome

AF:

0.0194

Gnomad ASJ exome

AF:

0.0350

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0311

Gnomad FIN exome

AF:

0.0536

Gnomad NFE exome

AF:

0.0694

Gnomad OTH exome

AF:

0.0440

GnomAD4 exome

AF:

0.0642

AC:

93834

AN:

1461528

Hom.:

3404

Cov.:

AF XY:

0.0637

AC XY:

46335

AN XY:

727040

show subpopulations

Gnomad4 AFR exome

AF:

0.00914

Gnomad4 AMR exome

AF:

0.0198

Gnomad4 ASJ exome

AF:

0.0361

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.0325

Gnomad4 FIN exome

AF:

0.0571

Gnomad4 NFE exome

AF:

0.0739

Gnomad4 OTH exome

AF:

0.0564

GnomAD4 genome

AF:

0.0447

AC:

6810

AN:

152332

Hom.:

251

Cov.:

AF XY:

0.0439

AC XY:

3269

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0115

Gnomad4 AMR

AF:

0.0266

Gnomad4 ASJ

AF:

0.0308

Gnomad4 EAS

AF:

0.000771

Gnomad4 SAS

AF:

0.0271

Gnomad4 FIN

AF:

0.0522

Gnomad4 NFE

AF:

0.0729

Gnomad4 OTH

AF:

0.0406

Alfa

AF:

0.0641

Hom.:

222

Bravo

AF:

0.0418

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.0672

EpiControl

AF:

0.0630

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ZNF512B-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Apr 15, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

8.2

DANN

Benign

0.86

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