chrX-7041142-C-G

Position:

• chrX-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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

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]

ACMG classification

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
PUDP	XR_001755734.2	n.550+36078G>C		intron_variant, non_coding_transcript_variant
PUDP	XR_007068202.1	n.550+36078G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PUDP	ENST00000655425.1	c.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

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

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

Other links and lift over

dbSNP: rs1852456; hg19: chrX-6959183;