chrX-7096726-C-T

Variant names:

• chrX-7096726-C-T
• rs5934477
• NM_012080.5:c.280+8894G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012080.5(PUDP):​c.280+8894G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0926 in 110,579 control chromosomes in the GnomAD database, including 465 homozygotes. There are 2,887 hemizygotes in GnomAD. 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 0.093 (465 hom., 2887 hem., cov: 22)
• Consequence: PUDP NM_012080.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 1 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PUDP	NM_012080.5	c.280+8894G>A		intron_variant	Intron 2 of 3	ENST00000381077.10	NP_036212.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PUDP	ENST00000381077.10	c.280+8894G>A		intron_variant	Intron 2 of 3	1	NM_012080.5	ENSP00000370467.6

Frequencies

GnomAD3 genomes AF: 0.0927 AC: 10242 AN: 110528 Hom.: 465 Cov.: 22

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.0686

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0127

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0940

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.117

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0926 AC: 10235 AN: 110579 Hom.: 465 Cov.: 22 AF XY: 0.0879 AC XY: 2887 AN XY: 32845

African (AFR) AF: 0.0214 AC: 652 AN: 30480

American (AMR) AF: 0.0684 AC: 713 AN: 10423

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 203 AN: 2621

East Asian (EAS) AF: 0.00 AC: 0 AN: 3516

South Asian (SAS) AF: 0.0120 AC: 31 AN: 2582

European-Finnish (FIN) AF: 0.133 AC: 767 AN: 5767

Middle Eastern (MID) AF: 0.0943 AC: 20 AN: 212

European-Non Finnish (NFE) AF: 0.142 AC: 7514 AN: 52794

Other (OTH) AF: 0.115 AC: 174 AN: 1511

Alfa AF: 0.107 Hom.: 692

Bravo AF: 0.0843

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.56
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5934477; hg19: chrX-7014767;