14-20474585-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000270.4(PNP):​c.285+10A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 1,609,246 control chromosomes in the GnomAD database, including 34,698 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4220 hom., cov: 32)
Exomes 𝑓: 0.20 ( 30478 hom. )

Consequence

PNP
NM_000270.4 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: -0.140
Variant links:
Genes affected
PNP (HGNC:7892): (purine nucleoside phosphorylase) This gene encodes an enzyme which reversibly catalyzes the phosphorolysis of purine nucleosides. The enzyme is trimeric, containing three identical subunits. Mutations which result in nucleoside phosphorylase deficiency result in defective T-cell (cell-mediated) immunity but can also affect B-cell immunity and antibody responses. Neurologic disorders may also be apparent in patients with immune defects. A known polymorphism at aa position 51 that does not affect enzyme activity has been described. A pseudogene has been identified on chromosome 2. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 14-20474585-A-G is Benign according to our data. Variant chr14-20474585-A-G is described in ClinVar as [Benign]. Clinvar id is 312730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-20474585-A-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PNPNM_000270.4 linkc.285+10A>G intron_variant Intron 3 of 5 ENST00000361505.10 NP_000261.2 P00491V9HWH6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PNPENST00000361505.10 linkc.285+10A>G intron_variant Intron 3 of 5 1 NM_000270.4 ENSP00000354532.6 P00491

Frequencies

GnomAD3 genomes
AF:
0.226
AC:
34319
AN:
151960
Hom.:
4209
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.315
Gnomad AMI
AF:
0.171
Gnomad AMR
AF:
0.184
Gnomad ASJ
AF:
0.188
Gnomad EAS
AF:
0.117
Gnomad SAS
AF:
0.146
Gnomad FIN
AF:
0.183
Gnomad MID
AF:
0.187
Gnomad NFE
AF:
0.205
Gnomad OTH
AF:
0.208
GnomAD3 exomes
AF:
0.189
AC:
47543
AN:
251404
Hom.:
4930
AF XY:
0.188
AC XY:
25539
AN XY:
135868
show subpopulations
Gnomad AFR exome
AF:
0.318
Gnomad AMR exome
AF:
0.145
Gnomad ASJ exome
AF:
0.186
Gnomad EAS exome
AF:
0.107
Gnomad SAS exome
AF:
0.158
Gnomad FIN exome
AF:
0.185
Gnomad NFE exome
AF:
0.206
Gnomad OTH exome
AF:
0.199
GnomAD4 exome
AF:
0.201
AC:
292589
AN:
1457168
Hom.:
30478
Cov.:
29
AF XY:
0.199
AC XY:
144582
AN XY:
725252
show subpopulations
Gnomad4 AFR exome
AF:
0.330
Gnomad4 AMR exome
AF:
0.153
Gnomad4 ASJ exome
AF:
0.190
Gnomad4 EAS exome
AF:
0.132
Gnomad4 SAS exome
AF:
0.158
Gnomad4 FIN exome
AF:
0.184
Gnomad4 NFE exome
AF:
0.205
Gnomad4 OTH exome
AF:
0.204
GnomAD4 genome
AF:
0.226
AC:
34367
AN:
152078
Hom.:
4220
Cov.:
32
AF XY:
0.222
AC XY:
16484
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.316
Gnomad4 AMR
AF:
0.184
Gnomad4 ASJ
AF:
0.188
Gnomad4 EAS
AF:
0.117
Gnomad4 SAS
AF:
0.146
Gnomad4 FIN
AF:
0.183
Gnomad4 NFE
AF:
0.205
Gnomad4 OTH
AF:
0.207
Alfa
AF:
0.212
Hom.:
2927
Bravo
AF:
0.231
Asia WGS
AF:
0.139
AC:
487
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:9
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Purine-nucleoside phosphorylase deficiency Benign:4
-
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Jan 13, 2018
Illumina Laboratory Services, Illumina
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 25, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not specified Benign:3
-
Clinical Genetics, Academic Medical Center
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

Mar 28, 2016
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Jan 24, 2024
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 36% of patients studied by a panel of primary immunodeficiencies. Number of patients: 34. Only high quality variants are reported. -

not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Mar 03, 2015
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
8.7
DANN
Benign
0.47

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1713420; hg19: chr14-20942744; COSMIC: COSV64092396; COSMIC: COSV64092396; API