rs10082685

Variant names:

• chr11-9522369-G-A
• rs10082685
• NM_003442.6:c.1687-2871G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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 Gene-Disease associations (from GenCC):

• methylmalonic aciduria and homocystinuria

  Inheritance: AR Classification: MODERATE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003442.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF143	NM_003442.6	MANE Select	c.1687-2871G>A		intron	N/A	NP_003433.3
	ZNF143	NM_001282656.2		c.1684-2871G>A		intron	N/A	NP_001269585.1
	ZNF143	NM_001282657.2		c.1594-2871G>A		intron	N/A	NP_001269586.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF143	ENST00000396602.7	TSL:1 MANE Select	c.1687-2871G>A		intron	N/A	ENSP00000379847.2
	ZNF143	ENST00000530463.5	TSL:1	c.1684-2871G>A		intron	N/A	ENSP00000432154.1
	ZNF143	ENST00000965750.1		c.1804-2871G>A		intron	N/A	ENSP00000635809.1

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

African (AFR) AF: 0.0133 AC: 550 AN: 41430

American (AMR) AF: 0.0362 AC: 551 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0668 AC: 231 AN: 3460

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5166

South Asian (SAS) AF: 0.0749 AC: 360 AN: 4808

European-Finnish (FIN) AF: 0.0610 AC: 639 AN: 10474

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0753 AC: 5113 AN: 67932

Other (OTH) AF: 0.0436 AC: 92 AN: 2112

Alfa AF: 0.0588 Hom.: 48

Bravo AF: 0.0453

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.54
DANN	Benign	0.25
PhyloP100		-0.84
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10082685; hg19: chr11-9543916;