Variant chrX-107628475-CG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The ENST00000643795(PRPS1):c.-153delG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000489 in 1,048,004 control chromosomes in the GnomAD database, including 5 homozygotes. There are 151 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00078 ( 0 hom., 26 hem., cov: 23)

Exomes 𝑓: 0.00045 ( 5 hom. 125 hem. )

Consequence

PRPS1
ENST00000643795 5_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:4

Conservation

PhyloP100: 1.96

Variant links:

Genes affected

PRPS1 (HGNC:9462): (phosphoribosyl pyrophosphate synthetase 1) This gene encodes an enzyme that catalyzes the phosphoribosylation of ribose 5-phosphate to 5-phosphoribosyl-1-pyrophosphate, which is necessary for purine metabolism and nucleotide biosynthesis. Defects in this gene are a cause of phosphoribosylpyrophosphate synthetase superactivity, Charcot-Marie-Tooth disease X-linked recessive type 5 and Arts Syndrome. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2011]

PRPS1 links:

PRPS1 (HGNC:):

PRPS1 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant X-107628475-CG-C is Benign according to our data. Variant chrX-107628475-CG-C is described in ClinVar as [Likely_benign]. Clinvar id is 367701.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 26 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
	use as main transcript	n.107628476delG	intergenic_region
PRPS1	NM_002764.4 linkuse as main transcript	c.-153delG	upstream_gene_variant	ENST00000372435.10	NP_002755.1	P60891-1
PRPS1	NM_001204402.2 linkuse as main transcript	c.-357delG	upstream_gene_variant		NP_001191331.1	P60891B7ZB02

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRPS1	ENST00000372435.10 linkuse as main transcript	c.-153delG		upstream_gene_variant		1	NM_002764.4	ENSP00000361512.4		P60891-1

Frequencies

GnomAD3 genomes

AF:

0.000795

AC:

AN:

111957

Hom.:

Cov.:

AF XY:

0.000762

AC XY:

AN XY:

34141

show subpopulations

Gnomad AFR

AF:

0.000520

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000474

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0183

Gnomad SAS

AF:

0.000746

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.000670

GnomAD4 exome

AF:

0.000454

AC:

425

AN:

935992

Hom.:

Cov.:

AF XY:

0.000470

AC XY:

125

AN XY:

265746

show subpopulations

Gnomad4 AFR exome

AF:

0.000217

Gnomad4 AMR exome

AF:

0.0000295

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00994

Gnomad4 SAS exome

AF:

0.000285

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000142

Gnomad4 OTH exome

AF:

0.00263

GnomAD4 genome

AF:

0.000777

AC:

AN:

112012

Hom.:

Cov.:

AF XY:

0.000760

AC XY:

AN XY:

34206

show subpopulations

Gnomad4 AFR

AF:

0.000518

Gnomad4 AMR

AF:

0.000473

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0178

Gnomad4 SAS

AF:

0.000749

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.000662

Alfa

AF:

0.000356

Hom.:

Bravo

AF:

0.000960

Asia WGS

AF:

0.00995

AC:

AN:

2522

ClinVar

Significance: Likely benign

Submissions summary: Benign:4

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Arts syndrome

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

X-linked nonsyndromic hearing loss

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Phosphoribosylpyrophosphate synthetase superactivity

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Charcot-Marie-Tooth, X-linked

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over