X-7041142-C-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000655425.1(PUDP):​c.204+36078G>C variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. 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 0.63 ( 15741 hom., 20464 hem., cov: 22)
Failed GnomAD Quality Control

Consequence

PUDP
ENST00000655425.1 intron, NMD_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0370
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PUDPXR_001755734.2 linkuse as main transcriptn.550+36078G>C intron_variant, non_coding_transcript_variant
PUDPXR_007068202.1 linkuse as main transcriptn.550+36078G>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PUDPENST00000655425.1 linkuse as main transcriptc.204+36078G>C intron_variant, NMD_transcript_variant ENSP00000499460

Frequencies

GnomAD3 genomes
AF:
0.631
AC:
69578
AN:
110267
Hom.:
15739
Cov.:
22
AF XY:
0.627
AC XY:
20401
AN XY:
32547
show subpopulations
Gnomad AFR
AF:
0.718
Gnomad AMI
AF:
0.315
Gnomad AMR
AF:
0.647
Gnomad ASJ
AF:
0.633
Gnomad EAS
AF:
0.598
Gnomad SAS
AF:
0.733
Gnomad FIN
AF:
0.537
Gnomad MID
AF:
0.600
Gnomad NFE
AF:
0.590
Gnomad OTH
AF:
0.611
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.631
AC:
69639
AN:
110320
Hom.:
15741
Cov.:
22
AF XY:
0.628
AC XY:
20464
AN XY:
32610
show subpopulations
Gnomad4 AFR
AF:
0.719
Gnomad4 AMR
AF:
0.648
Gnomad4 ASJ
AF:
0.633
Gnomad4 EAS
AF:
0.597
Gnomad4 SAS
AF:
0.734
Gnomad4 FIN
AF:
0.537
Gnomad4 NFE
AF:
0.590
Gnomad4 OTH
AF:
0.608
Alfa
AF:
0.625
Hom.:
4599
Bravo
AF:
0.639

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.8
DANN
Benign
0.77

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.

Other links and lift over

dbSNP: rs1852456; hg19: chrX-6959183; API