rs151124462
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_144709.4(PUS10):c.1482C>T(p.Phe494Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,734 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: 0.000016 ( 0 hom. )
Consequence
PUS10
NM_144709.4 synonymous
NM_144709.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.535
Publications
0 publications found
Genes affected
PUS10 (HGNC:26505): (pseudouridine synthase 10) Pseudouridination, the isomerization of uridine to pseudouridine, is the most common posttranscriptional nucleotide modification found in RNA and is essential for biologic functions such as spliceosome biogenesis. Pseudouridylate synthases, such as PUS10, catalyze pseudouridination of structural RNAs, including transfer, ribosomal, and splicing RNAs. These enzymes also act as RNA chaperones, facilitating the correct folding and assembly of tRNAs (McCleverty et al., 2007 [PubMed 17900615]).[supplied by OMIM, May 2009]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP7
Synonymous conserved (PhyloP=0.535 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_144709.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| PUS10 | NM_144709.4 | MANE Select | c.1482C>T | p.Phe494Phe | synonymous | Exon 17 of 18 | NP_653310.2 | Q3MIT2 | |
| PUS10 | NM_001322123.1 | c.1482C>T | p.Phe494Phe | synonymous | Exon 17 of 18 | NP_001309052.1 | Q3MIT2 | ||
| PUS10 | NM_001322124.1 | c.1482C>T | p.Phe494Phe | synonymous | Exon 17 of 18 | NP_001309053.1 | A8K6R4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PUS10 | ENST00000316752.11 | TSL:1 MANE Select | c.1482C>T | p.Phe494Phe | synonymous | Exon 17 of 18 | ENSP00000326003.6 | Q3MIT2 | |
| PUS10 | ENST00000602599.1 | TSL:1 | n.4085C>T | non_coding_transcript_exon | Exon 15 of 16 | ||||
| PUS10 | ENST00000971235.1 | c.1506C>T | p.Phe502Phe | synonymous | Exon 18 of 19 | ENSP00000641294.1 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152162
Hom.:
Cov.:
32
Gnomad AFR
AF:
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Gnomad OTH
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GnomAD2 exomes AF: 0.00000795 AC: 2AN: 251440 AF XY: 0.0000147 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
251440
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461572Hom.: 0 Cov.: 29 AF XY: 0.0000179 AC XY: 13AN XY: 727100 show subpopulations
GnomAD4 exome
AF:
AC:
23
AN:
1461572
Hom.:
Cov.:
29
AF XY:
AC XY:
13
AN XY:
727100
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33474
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26128
East Asian (EAS)
AF:
AC:
2
AN:
39690
South Asian (SAS)
AF:
AC:
1
AN:
86250
European-Finnish (FIN)
AF:
AC:
0
AN:
53410
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
20
AN:
1111746
Other (OTH)
AF:
AC:
0
AN:
60384
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.449
Heterozygous variant carriers
0
1
2
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0.00
0.20
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74336 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152162
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74336
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41438
American (AMR)
AF:
AC:
0
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5196
South Asian (SAS)
AF:
AC:
0
AN:
4830
European-Finnish (FIN)
AF:
AC:
0
AN:
10604
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
68032
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
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0.95
Allele balance
Alfa
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Hom.:
Bravo
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Asia WGS
AF:
AC:
1
AN:
3478
EpiCase
AF:
EpiControl
AF:
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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