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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PUDP	XR_001755734.2	n.840-59597A>G		intron_variant	Intron 5 of 5
PUDP	XR_007068202.1	n.840-61554A>G		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PUDP	ENST00000655425.1	n.*248-122799A>G		intron_variant	Intron 3 of 3			ENSP00000499460.1
ENSG00000297726	ENST00000750531.1	n.712-45763A>G		intron_variant	Intron 1 of 3
ENSG00000297726	ENST00000750532.1	n.645-45763A>G		intron_variant	Intron 1 of 2

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 v4.3

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;