19-37424330-G-A

Variant summary

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

The NM_152484.3(ZNF569):​c.238+1538C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,056 control chromosomes in the GnomAD database, including 1,223 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 0.11 ( 1223 hom., cov: 31)

Consequence

ZNF569
NM_152484.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.594
Variant links:
Genes affected
ZNF569 (HGNC:24737): (zinc finger protein 569) 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]

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=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF569NM_152484.3 linkuse as main transcriptc.238+1538C>T intron_variant ENST00000316950.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF569ENST00000316950.11 linkuse as main transcriptc.238+1538C>T intron_variant 1 NM_152484.3 P2Q5MCW4-1

Frequencies

GnomAD3 genomes
AF:
0.112
AC:
17040
AN:
151938
Hom.:
1224
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0301
Gnomad AMI
AF:
0.102
Gnomad AMR
AF:
0.106
Gnomad ASJ
AF:
0.155
Gnomad EAS
AF:
0.0808
Gnomad SAS
AF:
0.0807
Gnomad FIN
AF:
0.142
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.161
Gnomad OTH
AF:
0.116
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.112
AC:
17032
AN:
152056
Hom.:
1223
Cov.:
31
AF XY:
0.110
AC XY:
8208
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.0300
Gnomad4 AMR
AF:
0.106
Gnomad4 ASJ
AF:
0.155
Gnomad4 EAS
AF:
0.0810
Gnomad4 SAS
AF:
0.0806
Gnomad4 FIN
AF:
0.142
Gnomad4 NFE
AF:
0.161
Gnomad4 OTH
AF:
0.114
Alfa
AF:
0.147
Hom.:
353
Bravo
AF:
0.104
Asia WGS
AF:
0.103
AC:
357
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.66
DANN
Benign
0.63

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: rs1465434; hg19: chr19-37915232; API