ENST00000388829.3:n.224C>A

Variant names:

• chrX-13379117-G-T
• rs12557064
• ENST00000388829.3:n.224C>A

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 2 publications found

Genes affected

GPX1P1 (HGNC:4560): (glutathione peroxidase pseudogene 1)

ENSG00000294850 (HGNC:):

LINC01203 (HGNC:49634): (long intergenic non-protein coding RNA 1203)

ACMG classification

Our verdict: Likely_benign. The variant received -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 rank	MANE	Protein	UniProt
GPX1P1		n.13379117G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPX1P1	ENST00000388829.3	n.224C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000294850	ENST00000726311.1	n.40C>A		non_coding_transcript_exon_variant	Exon 1 of 2
LINC01203	ENST00000420403.2	n.249+1782G>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.000794 AC: 88 AN: 110900 Hom.: 1 Cov.: 23

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

African (AFR) AF: 0.000853 AC: 22 AN: 25786

American (AMR) AF: 0.00156 AC: 54 AN: 34598

Ashkenazi Jewish (ASJ) AF: 0.00566 AC: 106 AN: 18713

East Asian (EAS) AF: 0.00 AC: 0 AN: 29999

South Asian (SAS) AF: 0.000543 AC: 28 AN: 51527

European-Finnish (FIN) AF: 0.000101 AC: 4 AN: 39717

Middle Eastern (MID) AF: 0.0183 AC: 61 AN: 3325

European-Non Finnish (NFE) AF: 0.000494 AC: 380 AN: 769770

Other (OTH) AF: 0.00194 AC: 84 AN: 43371

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

African (AFR) AF: 0.0000978 AC: 3 AN: 30678

American (AMR) AF: 0.00113 AC: 12 AN: 10630

Ashkenazi Jewish (ASJ) AF: 0.00797 AC: 21 AN: 2634

East Asian (EAS) AF: 0.00 AC: 0 AN: 3508

South Asian (SAS) AF: 0.00 AC: 0 AN: 2596

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5801

Middle Eastern (MID) AF: 0.0276 AC: 6 AN: 217

European-Non Finnish (NFE) AF: 0.000835 AC: 44 AN: 52705

Other (OTH) AF: 0.00199 AC: 3 AN: 1508

Alfa AF: 0.00 Hom.: 2089

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
PhyloP100		6.8

Splicing

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

Other links and lift over

dbSNP: rs12557064; hg19: chrX-13397236;