rs4674324

Positions:

• chr2-218658710-T-G

Variant summary

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

The NM_001379659.1(ZNF142):​c.-44A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,980 control chromosomes in the GnomAD database, including 19,787 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 (19787 hom., cov: 31)
  • Exomes 𝑓: 0.65 (10 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF142 NM_001379659.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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]

BCS1L (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF142	NM_001379659.1	c.-44A>C		5_prime_UTR_variant	3/11	ENST00000411696.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF142	ENST00000411696.7	c.-44A>C		5_prime_UTR_variant	3/11	5	NM_001379659.1	P1

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70987 AN: 151862 Hom.: 19788 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.520

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.646 AC: 31 AN: 48 Hom.: 10 Cov.: 0 AF XY: 0.594 AC XY: 19 AN XY: 32

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.656

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.467 AC: 70978 AN: 151980 Hom.: 19787 Cov.: 31 AF XY: 0.475 AC XY: 35287 AN XY: 74290

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.520

Alfa AF: 0.540 Hom.: 8973

Bravo AF: 0.449

Asia WGS AF: 0.699 AC: 2430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.0
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs4674324; hg19: chr2-219523433;