3-125232327-CTTTTTT-CTTTTTTTT
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The ENST00000485866.5(ZNF148):c.*12_*13dupAA variant causes a splice region change involving the alteration of a non-conserved nucleotide. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000026 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ZNF148
ENST00000485866.5 splice_region
ENST00000485866.5 splice_region
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.285
Publications
1 publications found
Genes affected
ZNF148 (HGNC:12933): (zinc finger protein 148) The protein encoded by this gene is a member of the Kruppel family of zinc finger DNA binding proteins. The encoded protein activates transcription of the T-cell receptor and intestinal alkaline phosphatase genes but represses transcription of the ornithine decarboxylase, vimentin, gastrin, stomelysin, and enolase genes. Increased expression of this gene results in decreased patient survival rates from colorectal cancer, while mutations in this gene have been associated with global developmental delay, hypoplastic corpus callosum, and dysmorphic facies. [provided by RefSeq, Feb 2017]
ZNF148 Gene-Disease associations (from GenCC):
- global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic faciesInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000485866.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ZNF148 | NM_021964.3 | MANE Select | c.*12_*13dupAA | 3_prime_UTR | Exon 9 of 9 | NP_068799.2 | Q9UQR1-1 | ||
| ZNF148 | NM_001348424.1 | c.*12_*13dupAA | 3_prime_UTR | Exon 10 of 10 | NP_001335353.1 | Q9UQR1-1 | |||
| ZNF148 | NM_001348425.2 | c.*12_*13dupAA | 3_prime_UTR | Exon 10 of 10 | NP_001335354.1 | Q9UQR1-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ZNF148 | ENST00000485866.5 | TSL:1 | c.*12_*13dupAA | splice_region | Exon 10 of 10 | ENSP00000420448.1 | Q9UQR1-1 | ||
| ZNF148 | ENST00000360647.9 | TSL:1 MANE Select | c.*12_*13dupAA | 3_prime_UTR | Exon 9 of 9 | ENSP00000353863.4 | Q9UQR1-1 | ||
| ZNF148 | ENST00000484491.5 | TSL:1 | c.*12_*13dupAA | 3_prime_UTR | Exon 9 of 9 | ENSP00000420335.1 | Q9UQR1-1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 146570Hom.: 0 Cov.: 0
GnomAD3 genomes
AF:
AC:
0
AN:
146570
Hom.:
Cov.:
0
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:
GnomAD2 exomes AF: 0.0000591 AC: 9AN: 152218 AF XY: 0.0000360 show subpopulations
GnomAD2 exomes
AF:
AC:
9
AN:
152218
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000265 AC: 35AN: 1322666Hom.: 0 Cov.: 0 AF XY: 0.0000260 AC XY: 17AN XY: 653672 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
35
AN:
1322666
Hom.:
Cov.:
0
AF XY:
AC XY:
17
AN XY:
653672
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
29162
American (AMR)
AF:
AC:
2
AN:
35442
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22236
East Asian (EAS)
AF:
AC:
0
AN:
38000
South Asian (SAS)
AF:
AC:
7
AN:
73450
European-Finnish (FIN)
AF:
AC:
2
AN:
40176
Middle Eastern (MID)
AF:
AC:
1
AN:
5024
European-Non Finnish (NFE)
AF:
AC:
21
AN:
1024412
Other (OTH)
AF:
AC:
1
AN:
54764
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 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: 0.262
Heterozygous variant carriers
0
4
9
13
18
22
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
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Age
GnomAD4 genome 0.00 AC: 0AN: 146570Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 71136
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
146570
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
71136
African (AFR)
AF:
AC:
0
AN:
39776
American (AMR)
AF:
AC:
0
AN:
14714
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3414
East Asian (EAS)
AF:
AC:
0
AN:
5028
South Asian (SAS)
AF:
AC:
0
AN:
4652
European-Finnish (FIN)
AF:
AC:
0
AN:
9264
Middle Eastern (MID)
AF:
AC:
0
AN:
302
European-Non Finnish (NFE)
AF:
AC:
0
AN:
66506
Other (OTH)
AF:
AC:
0
AN:
2020
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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