rs2173724

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001001415.4(ZNF429):​c.4-3303A>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 151,900 control chromosomes in the GnomAD database, including 2,639 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 ( 2639 hom., cov: 32)

Consequence

ZNF429
NM_001001415.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.164
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
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 rank MANE Protein UniProt
ZNF429NM_001001415.4 linkc.4-3303A>G intron_variant Intron 1 of 3 ENST00000358491.9 NP_001001415.2 Q86V71

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF429ENST00000358491.9 linkc.4-3303A>G intron_variant Intron 1 of 3 3 NM_001001415.4 ENSP00000351280.3 Q86V71
ZNF429ENST00000597078.5 linkc.4-3303A>G intron_variant Intron 1 of 5 1 ENSP00000470300.1 M0QZ47
ZNF429ENST00000594022.1 linkn.193-2729A>G intron_variant Intron 2 of 5 3
ZNF429ENST00000596126.1 linkn.469-2729A>G intron_variant Intron 1 of 1 4

Frequencies

GnomAD3 genomes
AF:
0.186
AC:
28228
AN:
151782
Hom.:
2638
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.186
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:
0.223
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:
28236
AN:
151900
Hom.:
2639
Cov.:
32
AF XY:
0.186
AC XY:
13787
AN XY:
74210
show subpopulations
Gnomad4 AFR
AF:
0.186
Gnomad4 AMR
AF:
0.175
Gnomad4 ASJ
AF:
0.237
Gnomad4 EAS
AF:
0.0774
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.:
381
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
-0.81
CADD
Benign
6.9
DANN
Benign
0.83

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2173724; hg19: chr19-21709157; API