13-49496108-GGGGCGGGCGGGCGGGC-GGGGC
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_001419873.1(PHF11):c.-514_-503delCGGGCGGGCGGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000188 in 691,690 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000022 ( 0 hom. )
Consequence
PHF11
NM_001419873.1 5_prime_UTR
NM_001419873.1 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.703
Publications
1 publications found
Genes affected
PHF11 (HGNC:17024): (PHD finger protein 11) This gene encodes a protein containing a PHD (plant homeodomain) type zinc finger. This gene has been identified in some studies as a candidate gene for asthma. Naturally-occurring readthrough transcription may occur from the upstream SETDB2 (SET domain bifurcated 2) gene to this locus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
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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: NM_001419873.1. 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 |
|---|---|---|---|---|---|---|---|---|---|
| PHF11 | MANE Select | c.94+25_94+36delCGGGCGGGCGGG | intron | N/A | NP_001035533.1 | Q9UIL8-1 | |||
| PHF11 | c.-514_-503delCGGGCGGGCGGG | 5_prime_UTR | Exon 1 of 11 | NP_001406802.1 | Q9UIL8-2 | ||||
| PHF11 | c.-548_-537delCGGGCGGGCGGG | 5_prime_UTR | Exon 1 of 11 | NP_001406803.1 | Q9UIL8-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PHF11 | TSL:1 MANE Select | c.94+14_94+25delGGGCGGGCGGGC | intron | N/A | ENSP00000367570.3 | Q9UIL8-1 | |||
| PHF11 | c.94+14_94+25delGGGCGGGCGGGC | intron | N/A | ENSP00000611791.1 | |||||
| PHF11 | c.94+14_94+25delGGGCGGGCGGGC | intron | N/A | ENSP00000544049.1 |
Frequencies
GnomAD3 genomes 0.00000667 AC: 1AN: 149918Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
149918
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
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Gnomad SAS
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Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00 AC: 0AN: 94 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
94
AF XY:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.0000221 AC: 12AN: 541772Hom.: 0 AF XY: 0.0000149 AC XY: 4AN XY: 268140 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
12
AN:
541772
Hom.:
AF XY:
AC XY:
4
AN XY:
268140
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:
11704
American (AMR)
AF:
AC:
0
AN:
6992
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
10444
East Asian (EAS)
AF:
AC:
0
AN:
21778
South Asian (SAS)
AF:
AC:
1
AN:
22372
European-Finnish (FIN)
AF:
AC:
0
AN:
23542
Middle Eastern (MID)
AF:
AC:
0
AN:
1774
European-Non Finnish (NFE)
AF:
AC:
10
AN:
417812
Other (OTH)
AF:
AC:
0
AN:
25354
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000899368), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.350
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
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10
<30
30-35
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Age
GnomAD4 genome 0.00000667 AC: 1AN: 149918Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 73066 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:
149918
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
73066
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:
40840
American (AMR)
AF:
AC:
0
AN:
15160
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3464
East Asian (EAS)
AF:
AC:
0
AN:
4926
South Asian (SAS)
AF:
AC:
0
AN:
4766
European-Finnish (FIN)
AF:
AC:
0
AN:
10154
Middle Eastern (MID)
AF:
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67334
Other (OTH)
AF:
AC:
0
AN:
2070
⚠️ 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
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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