rs3752120

Variant names:

• chr19-52048768-C-T
• rs3752120
• NM_014650.4:c.-266G>A

Variant summary

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

The NM_014650.4(ZNF432):​c.-266G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,718 control chromosomes in the GnomAD database, including 2,181 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 0.15 (2174 hom., cov: 31)
  • Exomes 𝑓: 0.13 (7 hom.)
• Consequence: ZNF432 NM_014650.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

Genes affected

ZNF432 (HGNC:20810): (zinc finger protein 432) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000275055 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF432	NM_014650.4	c.-266G>A		5_prime_UTR_variant	Exon 1 of 5	ENST00000221315.10	NP_055465.1
ZNF432	NM_001322284.2	c.-352G>A		upstream_gene_variant			NP_001309213.1
ZNF432	NM_001322285.1	c.-420G>A		upstream_gene_variant			NP_001309214.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF432	ENST00000221315.10	c.-266G>A		5_prime_UTR_variant	Exon 1 of 5	1	NM_014650.4	ENSP00000221315.4

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22325 AN: 152064 Hom.: 2171 Cov.: 31

Gnomad AFR AF: 0.0532

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.156

GnomAD4 exome AF: 0.134 AC: 72 AN: 536 Hom.: 7 Cov.: 0 AF XY: 0.115 AC XY: 39 AN XY: 340

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.157

Gnomad4 NFE exome AF: 0.100

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.147 AC: 22352 AN: 152182 Hom.: 2174 Cov.: 31 AF XY: 0.152 AC XY: 11290 AN XY: 74388

Gnomad4 AFR AF: 0.0532

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.158

Alfa AF: 0.163 Hom.: 2620

Bravo AF: 0.144

Asia WGS AF: 0.322 AC: 1117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.5
DANN	Benign	0.76

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3752120; hg19: chr19-52552021;