19-21521677-T-G

Variant names:

• chr19-21521677-T-G
• rs1879234
• NM_001001415.4:c.4-7981T>G

Variant summary

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

The NM_001001415.4(ZNF429):​c.4-7981T>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 152,730 control chromosomes in the GnomAD database, including 50,334 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 (50111 hom., cov: 32)
  • Exomes 𝑓: 0.88 (223 hom.)
• Consequence: ZNF429 NM_001001415.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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]

BNIP3P26 (HGNC:49706): (BCL2 interacting protein 3 pseudogene 26)

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 rank	MANE	Protein	UniProt
ZNF429	NM_001001415.4	c.4-7981T>G		intron_variant	Intron 1 of 3	ENST00000358491.9	NP_001001415.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF429	ENST00000358491.9	c.4-7981T>G		intron_variant	Intron 1 of 3	3	NM_001001415.4	ENSP00000351280.3

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122577 AN: 152040 Hom.: 50071 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: 0.715

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.799

GnomAD4 exome AF: 0.879 AC: 503 AN: 572 Hom.: 223 Cov.: 0 AF XY: 0.870 AC XY: 261 AN XY: 300

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 SAS exome AF: 0.929

Gnomad4 FIN exome AF: 0.917

Gnomad4 NFE exome AF: 0.790

Gnomad4 OTH exome AF: 0.895

GnomAD4 genome AF: 0.806 AC: 122669 AN: 152158 Hom.: 50111 Cov.: 32 AF XY: 0.805 AC XY: 59868 AN XY: 74370

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.794

Alfa AF: 0.737 Hom.: 2532

Bravo AF: 0.809

Asia WGS AF: 0.739 AC: 2572 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	1.1
DANN	Benign	0.29

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: rs1879234; hg19: chr19-21704479;