rs1520071

Variant names:

• chr19-21519238-T-G
• rs1520071
• NM_001001415.4:c.4-10420T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001415.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF429	NM_001001415.4	MANE Select	c.4-10420T>G		intron	N/A	NP_001001415.2
	ZNF429	NR_144522.2		n.933T>G		non_coding_transcript_exon	Exon 3 of 3
	ZNF429	NR_144523.2		n.837T>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF429	ENST00000358491.9	TSL:3 MANE Select	c.4-10420T>G		intron	N/A	ENSP00000351280.3
	ZNF429	ENST00000597078.5	TSL:1	c.4-10420T>G		intron	N/A	ENSP00000470300.1
	ZNF429	ENST00000594022.1	TSL:3	n.193-9846T>G		intron	N/A

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

African (AFR) AF: 0.187 AC: 7748 AN: 41528

American (AMR) AF: 0.175 AC: 2678 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3466

East Asian (EAS) AF: 0.0773 AC: 400 AN: 5172

South Asian (SAS) AF: 0.181 AC: 873 AN: 4826

European-Finnish (FIN) AF: 0.192 AC: 2037 AN: 10598

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13137 AN: 67984

Other (OTH) AF: 0.187 AC: 395 AN: 2116

Alfa AF: 0.190 Hom.: 511

Bravo AF: 0.187

Asia WGS AF: 0.127 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.43
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1520071; hg19: chr19-21702040;