ENST00000442767.1:c.44+11839T>C

Variant names:

• chr17-76372007-A-G
• rs9909931
• ENST00000442767.1:c.44+11839T>C

Variant summary

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

The ENST00000442767.1(PRPSAP1):​c.44+11839T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,054 control chromosomes in the GnomAD database, including 6,018 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 0.26 (6018 hom., cov: 32)
• Consequence: PRPSAP1 ENST00000442767.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.87

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRPSAP1	ENST00000442767.1	c.44+11839T>C		intron_variant	Intron 1 of 3	5		ENSP00000402126.1
PRPSAP1	ENST00000423915.1	c.-140+12374T>C		intron_variant	Intron 1 of 4	4		ENSP00000409190.1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38847 AN: 151936 Hom.: 6005 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.256 AC: 38910 AN: 152054 Hom.: 6018 Cov.: 32 AF XY: 0.252 AC XY: 18767 AN XY: 74350

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.250

Alfa AF: 0.203 Hom.: 2046

Bravo AF: 0.267

Asia WGS AF: 0.236 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.090
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9909931; hg19: chr17-74368088;