2-218650036-A-G

Position:

• chr2-218650036-A-G

Variant summary

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

The NM_001379659.1(ZNF142):​c.1048+323T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,144 control chromosomes in the GnomAD database, including 19,794 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 0.47 (19794 hom., cov: 32)
• Consequence: ZNF142 NM_001379659.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

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=-0.85).
• 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	UniProt
ZNF142	NM_001379659.1	c.1048+323T>C		intron_variant		ENST00000411696.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF142	ENST00000411696.7	c.1048+323T>C		intron_variant		5	NM_001379659.1	P1

Frequencies

GnomAD3 genomes AF: 0.467 AC: 71034 AN: 152026 Hom.: 19795 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.467 AC: 71025 AN: 152144 Hom.: 19794 Cov.: 32 AF XY: 0.475 AC XY: 35318 AN XY: 74364

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.521

Alfa AF: 0.527 Hom.: 7746

Bravo AF: 0.449

Asia WGS AF: 0.699 AC: 2428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.72

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: rs10187066; hg19: chr2-219514759;