rs11077813

chr17-76340464-T-Cchr17-76340464-T-G

Variant summary

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

The NM_002766.3(PRPSAP1):c.290+4207A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 151,394 control chromosomes in the GnomAD database, including 4,284 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 0.21 (4284 hom., cov: 32)
• Consequence: PRPSAP1 NM_002766.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

Genes affected

PRPSAP1 (HGNC:9466): (phosphoribosyl pyrophosphate synthetase associated protein 1) Enables identical protein binding activity. Predicted to be involved in 5-phosphoribose 1-diphosphate biosynthetic process and purine nucleotide biosynthetic process. Predicted to be part of ribose phosphate diphosphokinase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRPSAP1	NM_002766.3	c.290+4207A>G		intron_variant		ENST00000446526.8
PRPSAP1	NM_001330503.2	c.-19-8029A>G		intron_variant
PRPSAP1	NM_001366236.2	c.-20+4207A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRPSAP1	ENST00000446526.8	c.290+4207A>G		intron_variant		1	NM_002766.3	P1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31271 AN: 151276 Hom.: 4287 Cov.: 32

Gnomad AFR AF: 0.0540

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.191

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.206 AC: 31261 AN: 151394 Hom.: 4284 Cov.: 32 AF XY: 0.212 AC XY: 15697 AN XY: 74000

Gnomad4 AFR AF: 0.0538

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.193

Alfa AF: 0.233 Hom.: 6866

Bravo AF: 0.189

Asia WGS AF: 0.357 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.096
Dann	Benign	0.76

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: rs11077813; hg19: chr17-74336545;