dbSNP rs771975802: UPRT:p.Asp128Asn (chrX-75274636-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_145052.4(UPRT):c.382G>A(p.Asp128Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000042 in 1,189,460 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000089 ( 0 hom., 1 hem., cov: 24)

Exomes 𝑓: 0.000045 ( 0 hom. 16 hem. )

Consequence

UPRT
NM_145052.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.46

Publications

0 publications found

Variant links:

Genes affected

UPRT (HGNC:28334): (uracil phosphoribosyltransferase homolog) This gene encodes uracil phosphoribosyltransferase, which catalyzes the conversion of uracil and 5-phosphoribosyl-1-R-diphosphate to uridine monophosphate (UMP). This reaction is an important part of nucleotide metabolism, specifically the pyrimidine salvage pathway. The enzyme localizes to the nucleus and cytoplasm. The protein is a potential target for rational design of drugs to treat parasitic infections and cancer. [provided by RefSeq, Nov 2009]

UPRT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Hemizygotes in GnomAdExome4 at 16 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145052.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
UPRT	NM_145052.4	MANE Select	c.382G>A	p.Asp128Asn	missense	Exon 1 of 7	NP_659489.1	Q96BW1-1
UPRT	NM_001307944.1		c.382G>A	p.Asp128Asn	missense	Exon 1 of 7	NP_001294873.1	A0A0A0MRR5
UPRT	NM_001363821.1		c.-22-18836G>A		intron	N/A	NP_001350750.1	E9PSD7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
UPRT	ENST00000373383.9	TSL:1 MANE Select	c.382G>A	p.Asp128Asn	missense	Exon 1 of 7	ENSP00000362481.4	Q96BW1-1
UPRT	ENST00000462237.5	TSL:1	n.382G>A		non_coding_transcript_exon	Exon 1 of 8	ENSP00000433987.1	Q96BW1-2
UPRT	ENST00000531704.5	TSL:1	n.552G>A		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.00000895

AC:

AN:

111794

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000188

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000894

AC:

AN:

156670

AF XY:

0.000153

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000189

Gnomad OTH exome

AF:

0.000255

GnomAD4 exome

AF:

0.0000455

AC:

AN:

1077666

Hom.:

Cov.:

AF XY:

0.0000461

AC XY:

AN XY:

347420

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

26069

American (AMR)

AF:

0.00

AC:

AN:

33351

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18167

East Asian (EAS)

AF:

0.0000335

AC:

AN:

29841

South Asian (SAS)

AF:

0.00

AC:

AN:

50682

European-Finnish (FIN)

AF:

0.00

AC:

AN:

39744

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4026

European-Non Finnish (NFE)

AF:

0.0000566

AC:

AN:

830596

Other (OTH)

AF:

0.0000221

AC:

AN:

45190

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00000895

AC:

AN:

111794

Hom.:

Cov.:

AF XY:

0.0000295

AC XY:

AN XY:

33954

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

30796

American (AMR)

AF:

0.00

AC:

AN:

10507

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2654

East Asian (EAS)

AF:

0.00

AC:

AN:

3547

South Asian (SAS)

AF:

0.00

AC:

AN:

2640

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6110

Middle Eastern (MID)

AF:

0.00

AC:

AN:

238

European-Non Finnish (NFE)

AF:

0.0000188

AC:

AN:

53126

Other (OTH)

AF:

0.00

AC:

AN:

1497

Age Distribution

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000142

Hom.:

Bravo

AF:

0.0000227

ExAC

AF:

0.000157

AC:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.40

BayesDel_addAF

Benign

-0.19

BayesDel_noAF

Benign

-0.23

CADD

Pathogenic

(source)

DANN

Pathogenic

1.0

DEOGEN2

Uncertain

0.59

FATHMM_MKL

Uncertain

0.84

LIST_S2

Pathogenic

0.99

M_CAP

Pathogenic

0.76

MetaRNN

Uncertain

0.66

MetaSVM

Pathogenic

0.85

MutationAssessor

Benign

1.5

PhyloP100

5.5

PrimateAI

Uncertain

0.77

PROVEAN

Uncertain

-3.8

REVEL

Pathogenic

0.73

Sift

Benign

0.12

Sift4G

Benign

0.12

Polyphen

0.94

Vest4

0.51

MVP

0.88

MPC

2.6

ClinPred

0.41

GERP RS

5.1

PromoterAI

-0.00090

Neutral

(source)

Varity_R

0.62

gMVP

0.91

Mutation Taster

=91/9

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over