Variant rs2043336 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173480.3(ZNF57):c.130+92T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 1,589,416 control chromosomes in the GnomAD database, including 593,747 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.84 ( 53559 hom., cov: 33)

Exomes 𝑓: 0.87 ( 540188 hom. )

Consequence

ZNF57
NM_173480.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.84

Variant links:

Genes affected

ZNF57 (HGNC:13125): (zinc finger protein 57) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF57 links:

(HGNC:):

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_addAF=-0.905119).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
ZNF57	NM_173480.3 linkuse as main transcript	c.130+92T>A	intron_variant	ENST00000306908.10	NP_775751.1
ZNF57	NM_001319083.2 linkuse as main transcript	c.34+92T>A	intron_variant		NP_001306012.1
ZNF57	XM_011527682.3 linkuse as main transcript	c.34+92T>A	intron_variant		XP_011525984.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF57	ENST00000306908.10 linkuse as main transcript	c.130+92T>A		intron_variant		1	NM_173480.3	ENSP00000303696	P1
	ENST00000654521.1 linkuse as main transcript	n.293-454A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.837

AC:

127302

AN:

152106

Hom.:

53545

Cov.:

show subpopulations

Gnomad AFR

AF:

0.770

Gnomad AMI

AF:

0.975

Gnomad AMR

AF:

0.846

Gnomad ASJ

AF:

0.754

Gnomad EAS

AF:

0.697

Gnomad SAS

AF:

0.802

Gnomad FIN

AF:

0.897

Gnomad MID

AF:

0.810

Gnomad NFE

AF:

0.883

Gnomad OTH

AF:

0.823

GnomAD3 exomes

AF:

0.843

AC:

209087

AN:

248012

Hom.:

88583

AF XY:

0.843

AC XY:

113258

AN XY:

134318

show subpopulations

Gnomad AFR exome

AF:

0.771

Gnomad AMR exome

AF:

0.860

Gnomad ASJ exome

AF:

0.765

Gnomad EAS exome

AF:

0.698

Gnomad SAS exome

AF:

0.805

Gnomad FIN exome

AF:

0.897

Gnomad NFE exome

AF:

0.879

Gnomad OTH exome

AF:

0.844

GnomAD4 exome

AF:

0.866

AC:

1244332

AN:

1437192

Hom.:

540188

Cov.:

AF XY:

0.864

AC XY:

618946

AN XY:

716352

show subpopulations

Gnomad4 AFR exome

AF:

0.757

Gnomad4 AMR exome

AF:

0.858

Gnomad4 ASJ exome

AF:

0.764

Gnomad4 EAS exome

AF:

0.747

Gnomad4 SAS exome

AF:

0.811

Gnomad4 FIN exome

AF:

0.896

Gnomad4 NFE exome

AF:

0.881

Gnomad4 OTH exome

AF:

0.837

GnomAD4 genome

AF:

0.837

AC:

127362

AN:

152224

Hom.:

53559

Cov.:

AF XY:

0.837

AC XY:

62302

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.769

Gnomad4 AMR

AF:

0.845

Gnomad4 ASJ

AF:

0.754

Gnomad4 EAS

AF:

0.697

Gnomad4 SAS

AF:

0.802

Gnomad4 FIN

AF:

0.897

Gnomad4 NFE

AF:

0.883

Gnomad4 OTH

AF:

0.820

Alfa

AF:

0.849

Hom.:

9713

Bravo

AF:

0.827

TwinsUK

AF:

0.877

AC:

3251

ALSPAC

AF:

0.871

AC:

3355

ExAC

AF:

0.842

AC:

102227

Asia WGS

AF:

0.749

AC:

2604

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.91

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.53

DANN

Benign

0.49

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.021

MutationTaster

Benign

1.0

P;P

GERP RS

-3.2

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over