X-6829265-T-C

Variant names:

• chrX-6829265-T-C
• rs5989586
• ENST00000655425.1:n.*248-122799A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000655425.1(PUDP):​n.*248-122799A>G variant causes a intron 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 0.52 (11301 hom., 16809 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: PUDP ENST00000655425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399
• Publications: 2 publications found

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]

ENSG00000297726 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655425.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PUDP	ENST00000655425.1		n.*248-122799A>G		intron	N/A	ENSP00000499460.1	A0A590UJH7
	ENSG00000297726	ENST00000750531.1		n.712-45763A>G		intron	N/A
	ENSG00000297726	ENST00000750532.1		n.645-45763A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.521 AC: 57306 AN: 110014 Hom.: 11299 Cov.: 22

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.464

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.506

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: 0.521 AC: 57357 AN: 110067 Hom.: 11301 Cov.: 22 AF XY: 0.519 AC XY: 16809 AN XY: 32383

African (AFR) AF: 0.685 AC: 20706 AN: 30231

American (AMR) AF: 0.426 AC: 4427 AN: 10393

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1066 AN: 2629

East Asian (EAS) AF: 0.773 AC: 2661 AN: 3443

South Asian (SAS) AF: 0.649 AC: 1639 AN: 2526

European-Finnish (FIN) AF: 0.520 AC: 3002 AN: 5771

Middle Eastern (MID) AF: 0.460 AC: 98 AN: 213

European-Non Finnish (NFE) AF: 0.429 AC: 22629 AN: 52692

Other (OTH) AF: 0.514 AC: 768 AN: 1495

Alfa AF: 0.429 Hom.: 10375

Bravo AF: 0.530

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.64
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs5989586; hg19: chrX-6747306;