Variant chr11-9472914-C-CT 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.205+162dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 322,256 control chromosomes in the GnomAD database, including 10,027 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.38 ( 9981 hom., cov: 0)

Exomes 𝑓: 0.24 ( 46 hom. )

Consequence

ZNF143
NM_003442.6 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.649

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 11-9472914-C-CT is Benign according to our data. Variant chr11-9472914-C-CT is described in ClinVar as [Benign]. Clinvar id is 1287822.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF143	NM_003442.6 link	c.205+162dupT		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.205+145_205+146insT		intron_variant		1	NM_003442.6	ENSP00000379847.2		P52747-1

Frequencies

GnomAD3 genomes

AF:

0.384

AC:

52247

AN:

136152

Hom.:

9984

Cov.:

show subpopulations

Gnomad AFR

AF:

0.254

Gnomad AMI

AF:

0.431

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.488

Gnomad EAS

AF:

0.276

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.461

Gnomad OTH

AF:

0.414

GnomAD4 exome

AF:

0.242

AC:

44973

AN:

186086

Hom.:

AF XY:

0.242

AC XY:

23311

AN XY:

96184

show subpopulations

Gnomad4 AFR exome

AF:

0.154

Gnomad4 AMR exome

AF:

0.239

Gnomad4 ASJ exome

AF:

0.263

Gnomad4 EAS exome

AF:

0.206

Gnomad4 SAS exome

AF:

0.202

Gnomad4 FIN exome

AF:

0.211

Gnomad4 NFE exome

AF:

0.255

Gnomad4 OTH exome

AF:

0.240

GnomAD4 genome

AF:

0.384

AC:

52249

AN:

136170

Hom.:

9981

Cov.:

AF XY:

0.376

AC XY:

24588

AN XY:

65394

show subpopulations

Gnomad4 AFR

AF:

0.254

Gnomad4 AMR

AF:

0.390

Gnomad4 ASJ

AF:

0.488

Gnomad4 EAS

AF:

0.277

Gnomad4 SAS

AF:

0.372

Gnomad4 FIN

AF:

0.349

Gnomad4 NFE

AF:

0.461

Gnomad4 OTH

AF:

0.416

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 25, 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