16-68566952-G-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000564558.5(ZFP90):n.*4080G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,036 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000012 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ZFP90
ENST00000564558.5 non_coding_transcript_exon
ENST00000564558.5 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.532
Publications
23 publications found
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]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000564558.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ZFP90 | NM_001305203.2 | MANE Select | c.*2254G>C | 3_prime_UTR | Exon 5 of 5 | NP_001292132.1 | |||
| ZFP90 | NR_130976.2 | n.4487G>C | non_coding_transcript_exon | Exon 5 of 5 | |||||
| ZFP90 | NR_130977.2 | n.4437G>C | non_coding_transcript_exon | Exon 5 of 5 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ZFP90 | ENST00000564558.5 | TSL:1 | n.*4080G>C | non_coding_transcript_exon | Exon 5 of 5 | ENSP00000457129.1 | |||
| ZFP90 | ENST00000563169.7 | TSL:1 MANE Select | c.*2254G>C | 3_prime_UTR | Exon 5 of 5 | ENSP00000454418.2 | |||
| ZFP90 | ENST00000570495.5 | TSL:1 | c.*2254G>C | 3_prime_UTR | Exon 5 of 5 | ENSP00000460547.1 |
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 152036Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152036
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000120 AC: 1AN: 833306Hom.: 0 Cov.: 54 AF XY: 0.00 AC XY: 0AN XY: 384832 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
833306
Hom.:
Cov.:
54
AF XY:
AC XY:
0
AN XY:
384832
show subpopulations
African (AFR)
AF:
AC:
0
AN:
15790
American (AMR)
AF:
AC:
0
AN:
984
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
5154
East Asian (EAS)
AF:
AC:
0
AN:
3768
South Asian (SAS)
AF:
AC:
0
AN:
16460
European-Finnish (FIN)
AF:
AC:
0
AN:
280
Middle Eastern (MID)
AF:
AC:
0
AN:
1620
European-Non Finnish (NFE)
AF:
AC:
1
AN:
761952
Other (OTH)
AF:
AC:
0
AN:
27298
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
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>80
Age
GnomAD4 genome 0.00000658 AC: 1AN: 152036Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74248 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
152036
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74248
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
41380
American (AMR)
AF:
AC:
0
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5192
South Asian (SAS)
AF:
AC:
0
AN:
4818
European-Finnish (FIN)
AF:
AC:
0
AN:
10600
Middle Eastern (MID)
AF:
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68002
Other (OTH)
AF:
AC:
0
AN:
2092
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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