rs1520071

Positions:

• chr19-21519238-T-G

Variant summary

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

The NM_001001415.4(ZNF429):​c.4-10420T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,192 control chromosomes in the GnomAD database, including 2,681 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 0.19 (2681 hom., cov: 33)
• Consequence: ZNF429 NM_001001415.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

Genes affected

ZNF429 (HGNC:20817): (zinc finger protein 429) 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. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF429	NM_001001415.4	c.4-10420T>G		intron_variant		ENST00000358491.9	NP_001001415.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF429	ENST00000358491.9	c.4-10420T>G		intron_variant		3	NM_001001415.4	ENSP00000351280	P1
ZNF429	ENST00000597078.5	c.4-10420T>G		intron_variant		1		ENSP00000470300
ZNF429	ENST00000594022.1	n.193-9846T>G		intron_variant, non_coding_transcript_variant		3
ZNF429	ENST00000596126.1	n.469-9846T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28320 AN: 152074 Hom.: 2680 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.186 AC: 28328 AN: 152192 Hom.: 2681 Cov.: 33 AF XY: 0.186 AC XY: 13853 AN XY: 74414

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0773

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.187

Alfa AF: 0.190 Hom.: 490

Bravo AF: 0.187

Asia WGS AF: 0.127 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.43

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: rs1520071; hg19: chr19-21702040;