dbSNP rs1737947: PRPSAP2:c.805-692A>G (chr17-18928119-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002767.4(PRPSAP2):c.805-692A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 153,224 control chromosomes in the GnomAD database, including 5,885 homozygotes. 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 0.27 ( 5815 hom., cov: 31)

Exomes 𝑓: 0.28 ( 70 hom. )

Consequence

PRPSAP2
NM_002767.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

Publications

9 publications found

Variant links:

Genes affected

PRPSAP2 (HGNC:9467): (phosphoribosyl pyrophosphate synthetase associated protein 2) This gene encodes a protein that associates with the enzyme phosphoribosylpyrophosphate synthetase (PRS). PRS catalyzes the formation of phosphoribosylpyrophosphate which is a substrate for synthesis of purine and pyrimidine nucleotides, histidine, tryptophan and NAD. PRS exists as a complex with two catalytic subunits and two associated subunits. This gene encodes a non-catalytic associated subunit of PRS. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]

PRPSAP2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRPSAP2	NM_002767.4 link	c.805-692A>G		intron_variant	Intron 10 of 11	ENST00000268835.7	NP_002758.1	O60256-1A0A024QYY3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRPSAP2	ENST00000268835.7 link	c.805-692A>G		intron_variant	Intron 10 of 11	1	NM_002767.4	ENSP00000268835.2		O60256-1

Frequencies

GnomAD3 genomes

AF:

0.273

AC:

41373

AN:

151776

Hom.:

5813

Cov.:

show subpopulations

Gnomad AFR

AF:

0.222

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.401

Gnomad FIN

AF:

0.302

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.308

Gnomad OTH

AF:

0.277

GnomAD4 exome

AF:

0.275

AC:

366

AN:

1330

Hom.:

AF XY:

0.251

AC XY:

177

AN XY:

704

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.144

AC:

AN:

208

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.154

AC:

AN:

South Asian (SAS)

AF:

0.338

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.302

AC:

289

AN:

958

Other (OTH)

AF:

0.240

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.524

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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

AF:

0.272

AC:

41383

AN:

151894

Hom.:

5815

Cov.:

AF XY:

0.274

AC XY:

20337

AN XY:

74240

show subpopulations

African (AFR)

AF:

0.222

AC:

9172

AN:

41380

American (AMR)

AF:

0.236

AC:

3595

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.267

AC:

925

AN:

3468

East Asian (EAS)

AF:

0.144

AC:

747

AN:

5176

South Asian (SAS)

AF:

0.401

AC:

1929

AN:

4812

European-Finnish (FIN)

AF:

0.302

AC:

3181

AN:

10550

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.308

AC:

20917

AN:

67938

Other (OTH)

AF:

0.276

AC:

582

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1515

3030

4544

6059

7574

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

440

880

1320

1760

2200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.302

Hom.:

3732

Bravo

AF:

0.260

Asia WGS

AF:

0.251

AC:

874

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.23

(source)

DANN

Benign

0.42

PhyloP100

-1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over