X-13379117-G-C

Position:

• chrX-13379117-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000388829.3(GPX1P1):​n.224C>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.531 in 110,886 control chromosomes in the GnomAD database, including 12,766 homozygotes. There are 17,275 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 0.53 (12766 hom., 17275 hem., cov: 23)
  • Exomes 𝑓: 0.61 (142409 hom. 170477 hem.)
  • Failed GnomAD Quality Control
• Consequence: GPX1P1 ENST00000388829.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.83

Genes affected

GPX1P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPX1P1		n.13379117G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPX1P1	ENST00000388829.3	n.224C>G		non_coding_transcript_exon_variant	1/1	6
LINC01203	ENST00000446964.1	n.148+1782G>C		intron_variant		2
LINC01203	ENST00000456091.2	n.1182+1782G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.531 AC: 58882 AN: 110834 Hom.: 12771 Cov.: 23 AF XY: 0.522 AC XY: 17256 AN XY: 33064

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.702

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.534

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.615 AC: 612050 AN: 995250 Hom.: 142409 Cov.: 27 AF XY: 0.581 AC XY: 170477 AN XY: 293276

Gnomad4 AFR exome AF: 0.255

Gnomad4 AMR exome AF: 0.358

Gnomad4 ASJ exome AF: 0.675

Gnomad4 EAS exome AF: 0.134

Gnomad4 SAS exome AF: 0.497

Gnomad4 FIN exome AF: 0.664

Gnomad4 NFE exome AF: 0.664

Gnomad4 OTH exome AF: 0.586

GnomAD4 genome AF: 0.531 AC: 58878 AN: 110886 Hom.: 12766 Cov.: 23 AF XY: 0.521 AC XY: 17275 AN XY: 33126

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.527

Alfa AF: 0.452 Hom.: 2089

Bravo AF: 0.505

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	7.5
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12557064; hg19: chrX-13397236;