rs1737947

chr17-18928119-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PRPSAP2	NM_002767.4	c.805-692A>G		intron_variant		ENST00000268835.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRPSAP2	ENST00000268835.7	c.805-692A>G		intron_variant		1	NM_002767.4	P1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41373 AN: 151776 Hom.: 5813 Cov.: 31

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.: 70 AF XY: 0.251 AC XY: 177 AN XY: 704

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.144

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.154

Gnomad4 SAS exome AF: 0.338

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.302

Gnomad4 OTH exome AF: 0.240

GnomAD4 genome AF: 0.272 AC: 41383 AN: 151894 Hom.: 5815 Cov.: 31 AF XY: 0.274 AC XY: 20337 AN XY: 74240

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.276

Alfa AF: 0.302 Hom.: 3317

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
Dann	Benign	0.42

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

Other links and lift over

dbSNP: rs1737947; hg19: chr17-18831432;