Variant chrX-22401155-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_073010.2(PTCHD1-AS):n.454-11435G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 111,143 control chromosomes in the GnomAD database, including 756 homozygotes. There are 3,809 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 0.12 ( 756 hom., 3809 hem., cov: 23)

Consequence

PTCHD1-AS
NR_073010.2 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.753

Variant links:

Genes affected

(HGNC:):

links:

PHEX (HGNC:8918): (phosphate regulating endopeptidase X-linked) The protein encoded by this gene is a transmembrane endopeptidase that belongs to the type II integral membrane zinc-dependent endopeptidase family. The protein is thought to be involved in bone and dentin mineralization and renal phosphate reabsorption. Mutations in this gene cause X-linked hypophosphatemic rickets. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

PHEX links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2 linkuse as main transcript	n.454-11435G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Protein
	ENST00000687248.1 linkuse as main transcript	n.454-11435G>A	intron_variant, non_coding_transcript_variant
PHEX	ENST00000683289.1 linkuse as main transcript	c.*28-24138C>T	intron_variant, NMD_transcript_variant	ENSP00000508195
	ENST00000687119.1 linkuse as main transcript	n.313-11435G>A	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

13084

AN:

111091

Hom.:

756

Cov.:

AF XY:

0.114

AC XY:

3801

AN XY:

33319

show subpopulations

Gnomad AFR

AF:

0.0292

Gnomad AMI

AF:

0.224

Gnomad AMR

AF:

0.0951

Gnomad ASJ

AF:

0.137

Gnomad EAS

AF:

0.0405

Gnomad SAS

AF:

0.205

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.162

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.132

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

GnomAD4 genome

AF:

0.118

AC:

13092

AN:

111143

Hom.:

756

Cov.:

AF XY:

0.114

AC XY:

3809

AN XY:

33381

show subpopulations

Gnomad4 AFR

AF:

0.0294

Gnomad4 AMR

AF:

0.0949

Gnomad4 ASJ

AF:

0.137

Gnomad4 EAS

AF:

0.0404

Gnomad4 SAS

AF:

0.206

Gnomad4 FIN

AF:

0.133

Gnomad4 NFE

AF:

0.170

Gnomad4 OTH

AF:

0.131

Alfa

AF:

0.134

Hom.:

937

Bravo

AF:

0.110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.67

DANN

Benign

0.72

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over