Variant chr19-47545853-G-A 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_001277075.3(ZNF541):c.676C>T(p.Leu226=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00946 in 1,549,642 control chromosomes in the GnomAD database, including 144 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0092 ( 22 hom., cov: 32)

Exomes 𝑓: 0.0095 ( 122 hom. )

Consequence

ZNF541
NM_001277075.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.861

Variant links:

Genes affected

ZNF541 (HGNC:25294): (zinc finger protein 541) Predicted to enable transcription corepressor activity. Predicted to be involved in histone deacetylation; negative regulation of transcription, DNA-templated; and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of histone deacetylase complex and transcription regulator complex. [provided by Alliance of Genome Resources, Apr 2022]

ZNF541 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=-0.49).

BP6

Variant 19-47545853-G-A is Benign according to our data. Variant chr19-47545853-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2650157.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.861 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 22 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF541	NM_001277075.3 linkuse as main transcript	c.676C>T	p.Leu226=	synonymous_variant	5/17	ENST00000391901.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF541	ENST00000391901.8 linkuse as main transcript	c.676C>T	p.Leu226=	synonymous_variant	5/17	5	NM_001277075.3	P1	Q9H0D2-3

Frequencies

GnomAD3 genomes

AF:

0.00918

AC:

1396

AN:

152136

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00162

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.00222

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.0497

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0106

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.0102

AC:

1519

AN:

148800

Hom.:

AF XY:

0.0102

AC XY:

818

AN XY:

79882

show subpopulations

Gnomad AFR exome

AF:

0.00137

Gnomad AMR exome

AF:

0.00187

Gnomad ASJ exome

AF:

0.00179

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00794

Gnomad FIN exome

AF:

0.0484

Gnomad NFE exome

AF:

0.00891

Gnomad OTH exome

AF:

0.00585

GnomAD4 exome

AF:

0.00950

AC:

13269

AN:

1397388

Hom.:

122

Cov.:

AF XY:

0.00951

AC XY:

6551

AN XY:

689130

show subpopulations

Gnomad4 AFR exome

AF:

0.000950

Gnomad4 AMR exome

AF:

0.00185

Gnomad4 ASJ exome

AF:

0.00231

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00788

Gnomad4 FIN exome

AF:

0.0449

Gnomad4 NFE exome

AF:

0.00916

Gnomad4 OTH exome

AF:

0.00780

GnomAD4 genome

AF:

0.00918

AC:

1397

AN:

152254

Hom.:

Cov.:

AF XY:

0.0106

AC XY:

787

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.00161

Gnomad4 AMR

AF:

0.00222

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00373

Gnomad4 FIN

AF:

0.0497

Gnomad4 NFE

AF:

0.0106

Gnomad4 OTH

AF:

0.00427

Alfa

AF:

0.00814

Hom.:

Bravo

AF:

0.00504

Asia WGS

AF:

0.00202

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

Oct 01, 2022

ZNF541: BP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

8.7

DANN

Benign

0.81

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