rs10498061

Positions:

• chr2-218647583-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF142	NM_001379659.1	c.1873+1052C>T		intron_variant		ENST00000411696.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF142	ENST00000411696.7	c.1873+1052C>T		intron_variant		5	NM_001379659.1	P1

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

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.0315

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.0439

Gnomad4 FIN AF: 0.0270

Gnomad4 NFE AF: 0.0339

Gnomad4 OTH AF: 0.0518

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.66

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: rs10498061; hg19: chr2-219512306;