rs10498061

Variant names:

• chr2-218647583-G-A
• rs10498061
• NM_001379659.1:c.1873+1052C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001379659.1(ZNF142):​c.1873+1052C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0566 in 152,092 control chromosomes in the GnomAD database, including 347 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 0.057 (347 hom., cov: 30)
• Consequence: ZNF142 NM_001379659.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 1 publications found

Genes affected

ZNF142 (HGNC:12927): (zinc finger protein 142) The protein encoded by this gene belongs to the Kruppel family of C2H2-type zinc finger proteins. It contains 31 C2H2-type zinc fingers and may be involved in transcriptional regulation. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2013]

ZNF142 Gene-Disease associations (from GenCC):

• neurodevelopmental disorder with impaired speech and hyperkinetic movements

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001379659.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF142	NM_001379659.1	MANE Select	c.1873+1052C>T		intron	N/A	NP_001366588.1
	ZNF142	NM_001366290.3		c.1873+1052C>T		intron	N/A	NP_001353219.1
	ZNF142	NM_001379660.1		c.1873+1052C>T		intron	N/A	NP_001366589.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF142	ENST00000411696.7	TSL:5 MANE Select	c.1873+1052C>T		intron	N/A	ENSP00000398798.3
	ZNF142	ENST00000449707.5	TSL:1	c.1273+1052C>T		intron	N/A	ENSP00000408643.1
	ZNF142	ENST00000450765.5	TSL:1	n.*1098+1052C>T		intron	N/A	ENSP00000397456.1

Frequencies

GnomAD3 genomes AF: 0.0565 AC: 8590 AN: 151974 Hom.: 346 Cov.: 30

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0314

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0438

Gnomad FIN AF: 0.0270

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0339

Gnomad OTH AF: 0.0523

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

GnomAD4 genome AF: 0.0566 AC: 8605 AN: 152092 Hom.: 347 Cov.: 30 AF XY: 0.0555 AC XY: 4128 AN XY: 74342

African (AFR) AF: 0.107 AC: 4447 AN: 41462

American (AMR) AF: 0.0315 AC: 482 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3470

East Asian (EAS) AF: 0.119 AC: 615 AN: 5170

South Asian (SAS) AF: 0.0439 AC: 211 AN: 4810

European-Finnish (FIN) AF: 0.0270 AC: 286 AN: 10586

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.0339 AC: 2303 AN: 68002

Other (OTH) AF: 0.0518 AC: 109 AN: 2106

Alfa AF: 0.0460 Hom.: 19

Bravo AF: 0.0593

Asia WGS AF: 0.0700 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.66
PhyloP100		0.31
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: rs10498061; hg19: chr2-219512306;