11-9471553-G-T

Position:

• chr11-9471553-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_003442.6(ZNF143):​c.112+133G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 466,658 control chromosomes in the GnomAD database, including 50,128 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.46 (16031 hom., cov: 30)
  • Exomes 𝑓: 0.47 (34097 hom.)
• Consequence: ZNF143 NM_003442.6 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.985

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant 11-9471553-G-T is Benign according to our data. Variant chr11-9471553-G-T is described in ClinVar as [Benign]. Clinvar id is 1274421.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF143	NM_003442.6	c.112+133G>T		intron_variant		ENST00000396602.7	NP_003433.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF143	ENST00000396602.7	c.112+133G>T		intron_variant		1	NM_003442.6	ENSP00000379847	P4

Frequencies

GnomAD3 genomes AF: 0.461 AC: 68752 AN: 149190 Hom.: 16032 Cov.: 30

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.473

GnomAD4 exome AF: 0.471 AC: 149634 AN: 317370 Hom.: 34097 AF XY: 0.471 AC XY: 77350 AN XY: 164178

Gnomad4 AFR exome AF: 0.366

Gnomad4 AMR exome AF: 0.442

Gnomad4 ASJ exome AF: 0.531

Gnomad4 EAS exome AF: 0.358

Gnomad4 SAS exome AF: 0.406

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.498

Gnomad4 OTH exome AF: 0.471

GnomAD4 genome AF: 0.461 AC: 68791 AN: 149288 Hom.: 16031 Cov.: 30 AF XY: 0.451 AC XY: 32833 AN XY: 72826

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.474

Alfa AF: 0.234 Hom.: 427

Bravo AF: 0.462

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 16, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.32

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

Other links and lift over

dbSNP: rs7119680; hg19: chr11-9493100;