rs1046152089
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005859.5(PURA):c.40G>A(p.Ala14Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000192 in 1,039,194 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A14P) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000011 ( 0 hom. )
Consequence
PURA
NM_005859.5 missense
NM_005859.5 missense
Scores
2
1
16
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.22
Publications
0 publications found
Genes affected
PURA (HGNC:9701): (purine rich element binding protein A) This gene product is a sequence-specific, single-stranded DNA-binding protein. It binds preferentially to the single strand of the purine-rich element termed PUR, which is present at origins of replication and in gene flanking regions in a variety of eukaryotes from yeasts through humans. Thus, it is implicated in the control of both DNA replication and transcription. Deletion of this gene has been associated with myelodysplastic syndrome and acute myelogenous leukemia. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.18423292).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.00000671 AC: 1AN: 148946Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
148946
Hom.:
Cov.:
31
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 AF: 0.00000112 AC: 1AN: 890248Hom.: 0 Cov.: 12 AF XY: 0.00000234 AC XY: 1AN XY: 427472 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
890248
Hom.:
Cov.:
12
AF XY:
AC XY:
1
AN XY:
427472
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
18218
American (AMR)
AF:
AC:
0
AN:
6910
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
11166
East Asian (EAS)
AF:
AC:
0
AN:
21952
South Asian (SAS)
AF:
AC:
0
AN:
16368
European-Finnish (FIN)
AF:
AC:
0
AN:
19794
Middle Eastern (MID)
AF:
AC:
0
AN:
2522
European-Non Finnish (NFE)
AF:
AC:
1
AN:
757620
Other (OTH)
AF:
AC:
0
AN:
35698
⚠️ 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: 0.275
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
70-75
75-80
>80
Age
GnomAD4 genome 0.00000671 AC: 1AN: 148946Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 72642 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
148946
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
72642
show subpopulations
African (AFR)
AF:
AC:
0
AN:
40490
American (AMR)
AF:
AC:
0
AN:
15008
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3434
East Asian (EAS)
AF:
AC:
0
AN:
5036
South Asian (SAS)
AF:
AC:
0
AN:
4690
European-Finnish (FIN)
AF:
AC:
0
AN:
10034
Middle Eastern (MID)
AF:
AC:
0
AN:
304
European-Non Finnish (NFE)
AF:
AC:
1
AN:
66996
Other (OTH)
AF:
AC:
0
AN:
2052
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
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.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of glycosylation at A14 (P = 0.0286);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.