Variant chr11-9471551-G-GT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_003442.6(ZNF143):c.112+132dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0985 in 491,192 control chromosomes in the GnomAD database, including 782 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.052 ( 265 hom., cov: 30)

Exomes 𝑓: 0.12 ( 517 hom. )

Consequence

ZNF143
NM_003442.6 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.560

Variant links:

Genes affected

ZNF143 (HGNC:12928): (zinc finger protein 143) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of snRNA transcription by RNA polymerase II. Predicted to be located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF143 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 11-9471551-G-GT is Benign according to our data. Variant chr11-9471551-G-GT is described in ClinVar as [Benign]. Clinvar id is 1280416.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.075 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF143	NM_003442.6 link	c.112+132dupT		intron_variant		ENST00000396602.7	NP_003433.3	P52747-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF143	ENST00000396602.7 link	c.112+131_112+132insT		intron_variant		1	NM_003442.6	ENSP00000379847.2		P52747-1

Frequencies

GnomAD3 genomes

AF:

0.0516

AC:

7696

AN:

149030

Hom.:

265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0137

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.0370

Gnomad ASJ

AF:

0.0743

Gnomad EAS

AF:

0.000584

Gnomad SAS

AF:

0.0776

Gnomad FIN

AF:

0.0627

Gnomad MID

AF:

0.0258

Gnomad NFE

AF:

0.0768

Gnomad OTH

AF:

0.0442

GnomAD4 exome

AF:

0.119

AC:

40685

AN:

342076

Hom.:

517

AF XY:

0.120

AC XY:

21254

AN XY:

176454

show subpopulations

Gnomad4 AFR exome

AF:

0.0666

Gnomad4 AMR exome

AF:

0.104

Gnomad4 ASJ exome

AF:

0.155

Gnomad4 EAS exome

AF:

0.0631

Gnomad4 SAS exome

AF:

0.116

Gnomad4 FIN exome

AF:

0.0943

Gnomad4 NFE exome

AF:

0.127

Gnomad4 OTH exome

AF:

0.124

GnomAD4 genome

AF:

0.0516

AC:

7695

AN:

149116

Hom.:

265

Cov.:

AF XY:

0.0507

AC XY:

3684

AN XY:

72712

show subpopulations

Gnomad4 AFR

AF:

0.0137

Gnomad4 AMR

AF:

0.0370

Gnomad4 ASJ

AF:

0.0743

Gnomad4 EAS

AF:

0.000585

Gnomad4 SAS

AF:

0.0772

Gnomad4 FIN

AF:

0.0627

Gnomad4 NFE

AF:

0.0768

Gnomad4 OTH

AF:

0.0443

Alfa

AF:

0.0234

Hom.:

Asia WGS

AF:

0.0400

AC:

138

AN:

3470

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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