rs2562408

chr19-21527079-C-Gchr19-21527079-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.4-2579C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,146 control chromosomes in the GnomAD database, including 50,123 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 0.81 (50123 hom., cov: 32)
• Consequence: ZNF429 NM_001001415.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF429	NM_001001415.4	c.4-2579C>G		intron_variant		ENST00000358491.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF429	ENST00000358491.9	c.4-2579C>G		intron_variant		3	NM_001001415.4	P1
ZNF429	ENST00000597078.5	c.4-2579C>G		intron_variant		1
ZNF429	ENST00000594022.1	n.193-2005C>G		intron_variant, non_coding_transcript_variant		3
ZNF429	ENST00000596126.1	n.469-2005C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122594 AN: 152028 Hom.: 50083 Cov.: 32

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.806 AC: 122686 AN: 152146 Hom.: 50123 Cov.: 32 AF XY: 0.805 AC XY: 59873 AN XY: 74368

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.794

Alfa AF: 0.788 Hom.: 5572

Bravo AF: 0.809

Asia WGS AF: 0.739 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.84
Dann	Benign	0.22

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: rs2562408; hg19: chr19-21709881;