Variant 20-53575878-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_006526.3(ZNF217):c.2886G>A(p.Pro962Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00645 in 1,614,204 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0067 ( 45 hom. )

Consequence

ZNF217
NM_006526.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.646

Variant links:

Genes affected

ZNF217 (HGNC:13009): (zinc finger protein 217) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in mitochondrion and nuclear speck. Part of histone deacetylase complex. [provided by Alliance of Genome Resources, Apr 2022]

ZNF217 links:

ENSG00000197670 (HGNC:):

ENSG00000197670 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 20-53575878-C-T is Benign according to our data. Variant chr20-53575878-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2652417.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.646 with no splicing effect.

BS2

High AC in GnomAd4 at 645 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF217	NM_006526.3 linkuse as main transcript	c.2886G>A	p.Pro962Pro	synonymous_variant	4/6	ENST00000371471.7	NP_006517.1	O75362

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZNF217	ENST00000371471.7 linkuse as main transcript	c.2886G>A	p.Pro962Pro	synonymous_variant	4/6	5	NM_006526.3	ENSP00000360526.2	O75362
ZNF217	ENST00000302342.3 linkuse as main transcript	c.2886G>A	p.Pro962Pro	synonymous_variant	3/5	1		ENSP00000304308.3	O75362
ZNF217	ENST00000437222.1 linkuse as main transcript	c.150G>A	p.Pro50Pro	synonymous_variant	1/2	2		ENSP00000394010.1	Q9BZ31
ENSG00000197670	ENST00000424252.2 linkuse as main transcript	n.*15C>T		downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.00424

AC:

645

AN:

152200

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00268

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000828

Gnomad FIN

AF:

0.00500

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00703

Gnomad OTH

AF:

0.00575

GnomAD3 exomes

AF:

0.00406

AC:

1021

AN:

251404

Hom.:

AF XY:

0.00428

AC XY:

582

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.00117

Gnomad AMR exome

AF:

0.00156

Gnomad ASJ exome

AF:

0.00159

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00150

Gnomad FIN exome

AF:

0.00462

Gnomad NFE exome

AF:

0.00664

Gnomad OTH exome

AF:

0.00505

GnomAD4 exome

AF:

0.00668

AC:

9765

AN:

1461886

Hom.:

Cov.:

AF XY:

0.00655

AC XY:

4764

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.00125

Gnomad4 AMR exome

AF:

0.00190

Gnomad4 ASJ exome

AF:

0.00111

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00189

Gnomad4 FIN exome

AF:

0.00446

Gnomad4 NFE exome

AF:

0.00798

Gnomad4 OTH exome

AF:

0.00512

GnomAD4 genome

AF:

0.00423

AC:

645

AN:

152318

Hom.:

Cov.:

AF XY:

0.00418

AC XY:

311

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00120

Gnomad4 AMR

AF:

0.00268

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000829

Gnomad4 FIN

AF:

0.00500

Gnomad4 NFE

AF:

0.00703

Gnomad4 OTH

AF:

0.00569

Alfa

AF:

0.00548

Hom.:

Bravo

AF:

0.00435

EpiCase

AF:

0.00611

EpiControl

AF:

0.00788

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

Sep 01, 2022

ZNF217: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

0.37

DANN

Benign

0.84

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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