rs1344528

Variant summary

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

The NM_001379286.1(ZNF423):​c.3849+15607C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,964 control chromosomes in the GnomAD database, including 30,660 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 0.62 ( 30660 hom., cov: 31)

Consequence

ZNF423
NM_001379286.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.307
Variant links:
Genes affected
ZNF423 (HGNC:16762): (zinc finger protein 423) The protein encoded by this gene is a nuclear protein that belongs to the family of Kruppel-like C2H2 zinc finger proteins. It functions as a DNA-binding transcription factor by using distinct zinc fingers in different signaling pathways. Thus, it is thought that this gene may have multiple roles in signal transduction during development. Mutations in this gene are associated with nephronophthisis-14 and Joubert syndrome-19. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF423NM_001379286.1 linkuse as main transcriptc.3849+15607C>A intron_variant ENST00000563137.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF423ENST00000563137.7 linkuse as main transcriptc.3849+15607C>A intron_variant 5 NM_001379286.1 P1

Frequencies

GnomAD3 genomes
AF:
0.621
AC:
94312
AN:
151846
Hom.:
30609
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.825
Gnomad AMI
AF:
0.630
Gnomad AMR
AF:
0.541
Gnomad ASJ
AF:
0.607
Gnomad EAS
AF:
0.592
Gnomad SAS
AF:
0.449
Gnomad FIN
AF:
0.559
Gnomad MID
AF:
0.582
Gnomad NFE
AF:
0.540
Gnomad OTH
AF:
0.615
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.621
AC:
94420
AN:
151964
Hom.:
30660
Cov.:
31
AF XY:
0.617
AC XY:
45822
AN XY:
74236
show subpopulations
Gnomad4 AFR
AF:
0.825
Gnomad4 AMR
AF:
0.542
Gnomad4 ASJ
AF:
0.607
Gnomad4 EAS
AF:
0.592
Gnomad4 SAS
AF:
0.447
Gnomad4 FIN
AF:
0.559
Gnomad4 NFE
AF:
0.540
Gnomad4 OTH
AF:
0.620
Alfa
AF:
0.547
Hom.:
25425
Bravo
AF:
0.634
Asia WGS
AF:
0.558
AC:
1943
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
0.21
DANN
Benign
0.31

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: rs1344528; hg19: chr16-49541928; API