Variant 20-63962351-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2

The NM_020713.3(ZNF512B):c.2187C>T(p.Leu729Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 1,612,670 control chromosomes in the GnomAD database, including 110 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.015 ( 14 hom., cov: 33)

Exomes 𝑓: 0.0099 ( 96 hom. )

Consequence

ZNF512B
NM_020713.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0520

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant 20-63962351-G-A is Benign according to our data. Variant chr20-63962351-G-A is described in ClinVar as [Benign]. Clinvar id is 3055650.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.052 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.015 (2278/152342) while in subpopulation AFR AF= 0.0274 (1140/41576). AF 95% confidence interval is 0.0261. There are 14 homozygotes in gnomad4. There are 1074 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 14 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF512B	NM_020713.3 linkuse as main transcript	c.2187C>T	p.Leu729Leu	synonymous_variant	14/17	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.2187C>T	p.Leu729Leu	synonymous_variant	14/17	1	NM_020713.3	ENSP00000358904.1		Q96KM6

Frequencies

GnomAD3 genomes

AF:

0.0149

AC:

2274

AN:

152224

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0274

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0167

Gnomad ASJ

AF:

0.00835

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.00489

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0108

Gnomad OTH

AF:

0.0220

GnomAD3 exomes

AF:

0.00934

AC:

2334

AN:

249770

Hom.:

AF XY:

0.00920

AC XY:

1245

AN XY:

135320

show subpopulations

Gnomad AFR exome

AF:

0.0280

Gnomad AMR exome

AF:

0.00934

Gnomad ASJ exome

AF:

0.00929

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00271

Gnomad FIN exome

AF:

0.00532

Gnomad NFE exome

AF:

0.0106

Gnomad OTH exome

AF:

0.0125

GnomAD4 exome

AF:

0.00991

AC:

14476

AN:

1460328

Hom.:

Cov.:

AF XY:

0.00967

AC XY:

7023

AN XY:

726510

show subpopulations

Gnomad4 AFR exome

AF:

0.0270

Gnomad4 AMR exome

AF:

0.0106

Gnomad4 ASJ exome

AF:

0.00858

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00253

Gnomad4 FIN exome

AF:

0.00607

Gnomad4 NFE exome

AF:

0.0103

Gnomad4 OTH exome

AF:

0.0114

GnomAD4 genome

AF:

0.0150

AC:

2278

AN:

152342

Hom.:

Cov.:

AF XY:

0.0144

AC XY:

1074

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.0274

Gnomad4 AMR

AF:

0.0167

Gnomad4 ASJ

AF:

0.00835

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.00489

Gnomad4 NFE

AF:

0.0108

Gnomad4 OTH

AF:

0.0218

Alfa

AF:

0.0122

Hom.:

Bravo

AF:

0.0164

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.0105

EpiControl

AF:

0.0110

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

Jun 25, 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

-0.44

CADD

Benign

5.5

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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