X-13379117-G-T

Position:

• chrX-13379117-G-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The ENST00000388829.3(GPX1P1):​n.224C>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.000802 in 110,952 control chromosomes in the GnomAD database, including 1 homozygotes. There are 20 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 0.00080 (1 hom., 20 hem., cov: 23)
  • Exomes 𝑓: 0.00073 (2 hom. 249 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 Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BS2: High Hemizygotes in GnomAd4 at 20 gene

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.000794 AC: 88 AN: 110900 Hom.: 1 Cov.: 23 AF XY: 0.000604 AC XY: 20 AN XY: 33092

Gnomad AFR AF: 0.0000653

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00113

Gnomad ASJ AF: 0.00797

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0252

Gnomad NFE AF: 0.000835

Gnomad OTH AF: 0.00201

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000727 AC: 739 AN: 1016806 Hom.: 2 Cov.: 27 AF XY: 0.000795 AC XY: 249 AN XY: 313206

Gnomad4 AFR exome AF: 0.000853

Gnomad4 AMR exome AF: 0.00156

Gnomad4 ASJ exome AF: 0.00566

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000543

Gnomad4 FIN exome AF: 0.000101

Gnomad4 NFE exome AF: 0.000494

Gnomad4 OTH exome AF: 0.00194

GnomAD4 genome AF: 0.000802 AC: 89 AN: 110952 Hom.: 1 Cov.: 23 AF XY: 0.000603 AC XY: 20 AN XY: 33154

Gnomad4 AFR AF: 0.0000978

Gnomad4 AMR AF: 0.00113

Gnomad4 ASJ AF: 0.00797

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000835

Gnomad4 OTH AF: 0.00199

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	7.3
DANN	Benign	0.89

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;