Variant chr19-47540323-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.2475C>T(p.Asn825=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0016 in 1,551,752 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 12 hom., cov: 31)

Exomes 𝑓: 0.0014 ( 32 hom. )

Consequence

ZNF541
NM_001277075.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.54

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=-0.93).

BP6

Variant 19-47540323-G-A is Benign according to our data. Variant chr19-47540323-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2650156.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.54 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF541	NM_001277075.3 linkuse as main transcript	c.2475C>T	p.Asn825=	synonymous_variant	7/17	ENST00000391901.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF541	ENST00000391901.8 linkuse as main transcript	c.2475C>T	p.Asn825=	synonymous_variant	7/17	5	NM_001277075.3	P1	Q9H0D2-3
ZNF541	ENST00000595558.1 linkuse as main transcript	c.1209C>T	p.Asn403=	synonymous_variant	3/12	1
ZNF541	ENST00000263351.9 linkuse as main transcript	c.1248C>T	p.Asn416=	synonymous_variant	3/7	1
ZNF541	ENST00000487275.1 linkuse as main transcript	n.90C>T		non_coding_transcript_exon_variant	2/5	3

Frequencies

GnomAD3 genomes

AF:

0.00316

AC:

481

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0385

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000955

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00402

AC:

643

AN:

159762

Hom.:

AF XY:

0.00369

AC XY:

309

AN XY:

83750

show subpopulations

Gnomad AFR exome

AF:

0.000223

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000885

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0351

Gnomad NFE exome

AF:

0.000533

Gnomad OTH exome

AF:

0.00175

GnomAD4 exome

AF:

0.00143

AC:

1997

AN:

1399460

Hom.:

Cov.:

AF XY:

0.00137

AC XY:

946

AN XY:

690178

show subpopulations

Gnomad4 AFR exome

AF:

0.0000950

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000560

Gnomad4 SAS exome

AF:

0.0000126

Gnomad4 FIN exome

AF:

0.0351

Gnomad4 NFE exome

AF:

0.000156

Gnomad4 OTH exome

AF:

0.00146

GnomAD4 genome

AF:

0.00316

AC:

481

AN:

152292

Hom.:

Cov.:

AF XY:

0.00493

AC XY:

367

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000131

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0385

Gnomad4 NFE

AF:

0.000955

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00111

Hom.:

Bravo

AF:

0.000208

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, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.11

DANN

Benign

0.46

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