2-218655682-C-T

Position:

• chr2-218655682-C-T

Variant summary

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

The NM_001367339.1(ZNF142):​c.*400G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,930 control chromosomes in the GnomAD database, including 20,491 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 0.49 (20491 hom., cov: 31)
• Consequence: ZNF142 NM_001367339.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF142	NM_001379659.1	c.280+468G>A		intron_variant		ENST00000411696.7	NP_001366588.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF142	ENST00000411696.7	c.280+468G>A		intron_variant		5	NM_001379659.1	ENSP00000398798.3

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74486 AN: 151812 Hom.: 20493 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.490 AC: 74484 AN: 151930 Hom.: 20491 Cov.: 31 AF XY: 0.499 AC XY: 37023 AN XY: 74250

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.537

Alfa AF: 0.522 Hom.: 2726

Bravo AF: 0.476

Asia WGS AF: 0.705 AC: 2449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
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: rs3931102; hg19: chr2-219520405;