rs1728785

Variant summary

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

The NM_001305203.2(ZFP90):​c.34-671A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 452,412 control chromosomes in the GnomAD database, including 139,911 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 ( 49518 hom., cov: 31)
Exomes 𝑓: 0.77 ( 90393 hom. )

Consequence

ZFP90
NM_001305203.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.323
Variant links:
Genes affected
ZFP90 (HGNC:23329): (ZFP90 zinc finger protein) This gene encodes a member of the zinc finger protein family that modulates gene expression. The encoded protein derepresses the transcription of certain fetal cardiac genes and may contribute to the genetic reprogramming that occurs during the development of heart failure. Genome wide association studies have identified this gene among ulcerative colitis risk loci. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Mar 2015]

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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZFP90NM_001305203.2 linkuse as main transcriptc.34-671A>C intron_variant ENST00000563169.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZFP90ENST00000563169.7 linkuse as main transcriptc.34-671A>C intron_variant 1 NM_001305203.2 P1Q8TF47-1

Frequencies

GnomAD3 genomes
AF:
0.805
AC:
122417
AN:
151982
Hom.:
49480
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.873
Gnomad AMI
AF:
0.826
Gnomad AMR
AF:
0.745
Gnomad ASJ
AF:
0.745
Gnomad EAS
AF:
0.817
Gnomad SAS
AF:
0.769
Gnomad FIN
AF:
0.843
Gnomad MID
AF:
0.797
Gnomad NFE
AF:
0.778
Gnomad OTH
AF:
0.774
GnomAD3 exomes
AF:
0.775
AC:
98777
AN:
127520
Hom.:
38350
AF XY:
0.776
AC XY:
54145
AN XY:
69806
show subpopulations
Gnomad AFR exome
AF:
0.876
Gnomad AMR exome
AF:
0.724
Gnomad ASJ exome
AF:
0.758
Gnomad EAS exome
AF:
0.815
Gnomad SAS exome
AF:
0.771
Gnomad FIN exome
AF:
0.832
Gnomad NFE exome
AF:
0.777
Gnomad OTH exome
AF:
0.769
GnomAD4 exome
AF:
0.775
AC:
232619
AN:
300314
Hom.:
90393
Cov.:
0
AF XY:
0.774
AC XY:
132059
AN XY:
170530
show subpopulations
Gnomad4 AFR exome
AF:
0.870
Gnomad4 AMR exome
AF:
0.722
Gnomad4 ASJ exome
AF:
0.756
Gnomad4 EAS exome
AF:
0.811
Gnomad4 SAS exome
AF:
0.770
Gnomad4 FIN exome
AF:
0.814
Gnomad4 NFE exome
AF:
0.777
Gnomad4 OTH exome
AF:
0.777
GnomAD4 genome
AF:
0.805
AC:
122511
AN:
152098
Hom.:
49518
Cov.:
31
AF XY:
0.807
AC XY:
60003
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.873
Gnomad4 AMR
AF:
0.745
Gnomad4 ASJ
AF:
0.745
Gnomad4 EAS
AF:
0.817
Gnomad4 SAS
AF:
0.769
Gnomad4 FIN
AF:
0.843
Gnomad4 NFE
AF:
0.778
Gnomad4 OTH
AF:
0.775
Alfa
AF:
0.776
Hom.:
67576
Bravo
AF:
0.802
Asia WGS
AF:
0.732
AC:
2547
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
6.0
DANN
Benign
0.68

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: rs1728785; hg19: chr16-68591230; API