Variant chrX-13379117-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The ENST00000388829.3(GPX1P1):n.224C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.000363 in 1,127,755 control chromosomes in the GnomAD database, including 3 homozygotes. There are 100 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 0.0020 ( 2 hom., 66 hem., cov: 23)

Exomes 𝑓: 0.00018 ( 1 hom. 34 hem. )

Consequence

GPX1P1
ENST00000388829.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.83

Variant links:

Genes affected

GPX1P1 (HGNC:):

GPX1P1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPX1P1	use as main transcript	n.13379117G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
GPX1P1	ENST00000388829.3 linkuse as main transcript	n.224C>T	non_coding_transcript_exon_variant	1/1	6
LINC01203	ENST00000446964.1 linkuse as main transcript	n.148+1782G>A	intron_variant		2
LINC01203	ENST00000456091.2 linkuse as main transcript	n.1182+1782G>A	intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00199

AC:

221

AN:

110900

Hom.:

Cov.:

AF XY:

0.00196

AC XY:

AN XY:

33092

show subpopulations

Gnomad AFR

AF:

0.00693

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000471

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000190

Gnomad OTH

AF:

0.00201

GnomAD4 exome

AF:

0.000184

AC:

187

AN:

1016803

Hom.:

Cov.:

AF XY:

0.000109

AC XY:

AN XY:

313205

show subpopulations

Gnomad4 AFR exome

AF:

0.00609

Gnomad4 AMR exome

AF:

0.000405

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000130

Gnomad4 OTH exome

AF:

0.000346

GnomAD4 genome

AF:

0.00200

AC:

222

AN:

110952

Hom.:

Cov.:

AF XY:

0.00199

AC XY:

AN XY:

33154

show subpopulations

Gnomad4 AFR

AF:

0.00694

Gnomad4 AMR

AF:

0.000470

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000190

Gnomad4 OTH

AF:

0.00199

Alfa

AF:

0.0000951

Hom.:

2089

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

7.7

DANN

Benign

0.94

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