17-18850557-C-T

Variant names:

• chr17-18850557-C-T
• rs4924935
• ENST00000441887.5:c.-33+8193C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000800191.1(ENSG00000289213):​n.189+5487G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,038 control chromosomes in the GnomAD database, including 41,187 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 0.73 (41187 hom., cov: 31)
• Consequence: ENSG00000289213 ENST00000800191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 35 publications found

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]

ENSG00000289213 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000800191.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRPSAP2	ENST00000441887.5	TSL:5	c.-33+8193C>T		intron	N/A	ENSP00000395127.1
	ENSG00000289213	ENST00000800191.1		n.189+5487G>A		intron	N/A
	ENSG00000289213	ENST00000800192.1		n.164+5487G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111414 AN: 151920 Hom.: 41133 Cov.: 31

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.734 AC: 111528 AN: 152038 Hom.: 41187 Cov.: 31 AF XY: 0.732 AC XY: 54336 AN XY: 74278

African (AFR) AF: 0.804 AC: 33320 AN: 41464

American (AMR) AF: 0.767 AC: 11716 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2527 AN: 3468

East Asian (EAS) AF: 0.853 AC: 4407 AN: 5166

South Asian (SAS) AF: 0.582 AC: 2801 AN: 4816

European-Finnish (FIN) AF: 0.697 AC: 7358 AN: 10556

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46987 AN: 67976

Other (OTH) AF: 0.734 AC: 1545 AN: 2106

Alfa AF: 0.709 Hom.: 182366

Bravo AF: 0.748

Asia WGS AF: 0.744 AC: 2589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.38
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs4924935; hg19: chr17-18753870;