11-9472519-C-T

Position:

• chr11-9472519-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003442.6(ZNF143):​c.113-158C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,028 control chromosomes in the GnomAD database, including 2,666 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.17 (2666 hom., cov: 33)
• Consequence: ZNF143 NM_003442.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.43

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BP6: Variant 11-9472519-C-T is Benign according to our data. Variant chr11-9472519-C-T is described in ClinVar as [Benign]. Clinvar id is 1228189.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF143	NM_003442.6	c.113-158C>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.113-158C>T		intron_variant		1	NM_003442.6	ENSP00000379847	P4

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25555 AN: 151910 Hom.: 2662 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0992

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.00539

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.153

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.168 AC: 25584 AN: 152028 Hom.: 2666 Cov.: 33 AF XY: 0.163 AC XY: 12084 AN XY: 74316

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.0991

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.00541

Gnomad4 SAS AF: 0.0723

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.152

Alfa AF: 0.162 Hom.: 287

Bravo AF: 0.171

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.78

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: rs12361328; hg19: chr11-9494066;