chr8-31032733-C-T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_001323311.2(PURG):​c.50G>A​(p.Gly17Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,299,282 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000062 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PURG
NM_001323311.2 missense

Scores

1
2
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.04

Publications

1 publications found
Variant links:
Genes affected
PURG (HGNC:17930): (purine rich element binding protein G) The exact function of this gene is not known, however, its encoded product is highly similar to purine-rich element binding protein A. The latter is a DNA-binding protein which binds preferentially to the single strand of the purine-rich element termed PUR, and has been implicated in the control of both DNA replication and transcription. This gene lies in close proximity to the Werner syndrome gene, but on the opposite strand, on chromosome 8p11. [provided by RefSeq, Apr 2016]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.114308566).
BS2
High AC in GnomAdExome4 at 8 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PURGNM_001323311.2 linkc.50G>A p.Gly17Asp missense_variant Exon 2 of 2 ENST00000523392.2 NP_001310240.1 Q9UJV8-1
PURGNM_013357.2 linkc.50G>A p.Gly17Asp missense_variant Exon 1 of 1 NP_037489.1 Q9UJV8-1
PURGNM_001015508.3 linkc.50G>A p.Gly17Asp missense_variant Exon 1 of 2 NP_001015508.1 Q9UJV8-2
PURGNM_001323312.2 linkc.50G>A p.Gly17Asp missense_variant Exon 2 of 3 NP_001310241.1 Q9UJV8-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PURGENST00000523392.2 linkc.50G>A p.Gly17Asp missense_variant Exon 2 of 2 3 NM_001323311.2 ENSP00000466881.2 Q9UJV8-1K7ENC1
PURGENST00000339382.3 linkc.50G>A p.Gly17Asp missense_variant Exon 1 of 2 1 ENSP00000345168.2 Q9UJV8-2
PURGENST00000475541.2 linkc.50G>A p.Gly17Asp missense_variant Exon 1 of 1 6 ENSP00000418721.1 Q9UJV8-1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
151936
Hom.:
0
Cov.:
32
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD2 exomes
AF:
0.0000211
AC:
2
AN:
94662
AF XY:
0.0000206
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000490
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000616
AC:
8
AN:
1299282
Hom.:
0
Cov.:
32
AF XY:
0.00000635
AC XY:
4
AN XY:
629986
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
28890
American (AMR)
AF:
0.00
AC:
0
AN:
21154
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
18720
East Asian (EAS)
AF:
0.00
AC:
0
AN:
36180
South Asian (SAS)
AF:
0.0000165
AC:
1
AN:
60464
European-Finnish (FIN)
AF:
0.0000448
AC:
2
AN:
44618
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4094
European-Non Finnish (NFE)
AF:
0.00000485
AC:
5
AN:
1031756
Other (OTH)
AF:
0.00
AC:
0
AN:
53406
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.538
Heterozygous variant carriers
0
1
2
2
3
4
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
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
151936
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74212
African (AFR)
AF:
0.00
AC:
0
AN:
41418
American (AMR)
AF:
0.00
AC:
0
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3466
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5144
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4834
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10568
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67924
Other (OTH)
AF:
0.00
AC:
0
AN:
2090
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000119
AC:
1
ExAC
AF:
0.0000186
AC:
2

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Apr 15, 2025
Ambry Genetics
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The c.50G>A (p.G17D) alteration is located in exon 1 (coding exon 1) of the PURG gene. This alteration results from a G to A substitution at nucleotide position 50, causing the glycine (G) at amino acid position 17 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.34
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
21
DANN
Benign
0.96
DEOGEN2
Benign
0.039
.;T;.
Eigen
Benign
-0.19
Eigen_PC
Benign
-0.11
FATHMM_MKL
Uncertain
0.85
D
LIST_S2
Benign
0.76
T;T;T
M_CAP
Benign
0.028
D
MetaRNN
Benign
0.11
T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.55
N;N;.
PhyloP100
1.0
PrimateAI
Pathogenic
0.80
T
PROVEAN
Benign
-1.0
N;N;.
REVEL
Benign
0.072
Sift
Benign
0.26
T;T;.
Sift4G
Benign
0.11
T;T;.
Polyphen
0.85
P;P;.
Vest4
0.24
MVP
0.082
MPC
1.1
ClinPred
0.17
T
GERP RS
2.4
Varity_R
0.13
gMVP
0.48
Mutation Taster
=83/17
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs371187359; hg19: chr8-30890249; API