rs1984771

chr19-21508995-C-T

Variant summary

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

The NM_001001415.4(ZNF429):c.3+3221C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,744 control chromosomes in the GnomAD database, including 2,997 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 0.20 (2997 hom., cov: 31)
• Consequence: ZNF429 NM_001001415.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF429	NM_001001415.4	c.3+3221C>T		intron_variant		ENST00000358491.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF429	ENST00000358491.9	c.3+3221C>T		intron_variant		3	NM_001001415.4	P1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29754 AN: 151628 Hom.: 2988 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.0768

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.196 AC: 29791 AN: 151744 Hom.: 2997 Cov.: 31 AF XY: 0.196 AC XY: 14555 AN XY: 74120

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.0769

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.193

Alfa AF: 0.194 Hom.: 3129

Bravo AF: 0.198

Asia WGS AF: 0.132 AC: 458 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	5.0
Dann	Benign	0.70

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: rs1984771; hg19: chr19-21691797;