11-9522369-G-A

Position:

• chr11-9522369-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003442.6(ZNF143):​c.1687-2871G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0503 in 151,816 control chromosomes in the GnomAD database, including 266 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 0.050 (266 hom., cov: 32)
• Consequence: ZNF143 NM_003442.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF143	NM_003442.6	c.1687-2871G>A		intron_variant		ENST00000396602.7	NP_003433.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF143	ENST00000396602.7	c.1687-2871G>A		intron_variant		1	NM_003442.6	ENSP00000379847	P4

Frequencies

GnomAD3 genomes AF: 0.0504 AC: 7642 AN: 151698 Hom.: 266 Cov.: 32

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0362

Gnomad ASJ AF: 0.0668

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0752

Gnomad FIN AF: 0.0610

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0753

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0503 AC: 7640 AN: 151816 Hom.: 266 Cov.: 32 AF XY: 0.0495 AC XY: 3668 AN XY: 74166

Gnomad4 AFR AF: 0.0133

Gnomad4 AMR AF: 0.0362

Gnomad4 ASJ AF: 0.0668

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0749

Gnomad4 FIN AF: 0.0610

Gnomad4 NFE AF: 0.0753

Gnomad4 OTH AF: 0.0436

Alfa AF: 0.0597 Hom.: 47

Bravo AF: 0.0453

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.54
DANN	Benign	0.25

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: rs10082685; hg19: chr11-9543916;