Genetic Variant PUDP:c.511-7262A>G (chrX-7057734-T-C) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001178135.2(PUDP):c.600A>G(p.Gln200Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000192 in 1,150,478 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 62 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000055 ( 0 hom., 0 hem., cov: 21)

Exomes 𝑓: 0.00021 ( 0 hom. 62 hem. )

Consequence

PUDP
NM_001178135.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.147

Publications

0 publications found

Variant links:

Genes affected

PUDP (HGNC:16818): (pseudouridine 5'-phosphatase) This gene encodes a member of the haloacid dehalogenase-like (HAD) hydrolase superfamily. The encoded protein has no known biological function. This gene has a pseudogene on chromosome 1. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2010]

PUDP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BP6

Variant X-7057734-T-C is Benign according to our data. Variant chrX-7057734-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2659912.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.147 with no splicing effect.

BS2

High Hemizygotes in GnomAdExome4 at 62 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001178135.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PUDP	NM_012080.5	MANE Select	c.511-7262A>G		intron	N/A	NP_036212.3	Q08623-1
PUDP	NM_001178135.2		c.600A>G	p.Gln200Gln	synonymous	Exon 4 of 4	NP_001171606.1	Q08623-3
PUDP	NM_001135565.2		c.580-7262A>G		intron	N/A	NP_001129037.1	Q08623-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PUDP	ENST00000381077.10	TSL:1 MANE Select	c.511-7262A>G		intron	N/A	ENSP00000370467.6	Q08623-1
PUDP	ENST00000486446.3	TSL:2	c.600A>G	p.Gln200Gln	synonymous	Exon 4 of 4	ENSP00000430995.2	Q08623-3
PUDP	ENST00000424830.6	TSL:3	c.580-7262A>G		intron	N/A	ENSP00000396452.2	Q08623-4

Frequencies

GnomAD3 genomes

AF:

0.0000551

AC:

AN:

108847

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000671

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000198

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:

0.0000381

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000102

AC:

AN:

97968

AF XY:

0.0000274

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000519

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000246

Gnomad NFE exome

AF:

0.000208

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000206

AC:

215

AN:

1041631

Hom.:

Cov.:

AF XY:

0.000182

AC XY:

AN XY:

340571

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

24899

American (AMR)

AF:

0.0000358

AC:

AN:

27905

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18635

East Asian (EAS)

AF:

0.00

AC:

AN:

27128

South Asian (SAS)

AF:

0.0000201

AC:

AN:

49863

European-Finnish (FIN)

AF:

0.0000769

AC:

AN:

26024

Middle Eastern (MID)

AF:

0.000489

AC:

AN:

4087

European-Non Finnish (NFE)

AF:

0.000249

AC:

204

AN:

818817

Other (OTH)

AF:

0.000113

AC:

AN:

44273

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

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:

0.0000551

AC:

AN:

108847

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

31211

show subpopulations

African (AFR)

AF:

0.0000671

AC:

AN:

29803

American (AMR)

AF:

0.000198

AC:

AN:

10089

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2627

East Asian (EAS)

AF:

0.00

AC:

AN:

3416

South Asian (SAS)

AF:

0.00

AC:

AN:

2426

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5620

Middle Eastern (MID)

AF:

0.00

AC:

AN:

236

European-Non Finnish (NFE)

AF:

0.0000381

AC:

AN:

52481

Other (OTH)

AF:

0.00

AC:

AN:

1471

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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:

0.00

Hom.:

Bravo

AF:

0.0000491

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.1

(source)

DANN

Benign

0.49

PhyloP100

0.15

Mutation Taster

=100/0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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