X-13379117-G-A

Variant names:

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

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>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
• 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=-0.39).
• BS2: High Homozygotes in GnomAd4 at 2 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000388829.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPX1P1	ENST00000388829.3	TSL:6	n.224C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000294850	ENST00000726311.1		n.40C>T		non_coding_transcript_exon	Exon 1 of 2
	LINC01203	ENST00000420403.2	TSL:3	n.249+1782G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00199 AC: 221 AN: 110900 Hom.: 2 Cov.: 23

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.: 1 Cov.: 27 AF XY: 0.000109 AC XY: 34 AN XY: 313205

African (AFR) AF: 0.00609 AC: 157 AN: 25778

American (AMR) AF: 0.000405 AC: 14 AN: 34599

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18713

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

South Asian (SAS) AF: 0.00 AC: 0 AN: 51527

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39717

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3325

European-Non Finnish (NFE) AF: 0.00000130 AC: 1 AN: 769774

Other (OTH) AF: 0.000346 AC: 15 AN: 43371

GnomAD4 genome AF: 0.00200 AC: 222 AN: 110952 Hom.: 2 Cov.: 23 AF XY: 0.00199 AC XY: 66 AN XY: 33154

African (AFR) AF: 0.00694 AC: 213 AN: 30678

American (AMR) AF: 0.000470 AC: 5 AN: 10630

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 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: 0.00 AC: 0 AN: 217

European-Non Finnish (NFE) AF: 0.0000190 AC: 1 AN: 52705

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

Alfa AF: 0.0000951 Hom.: 2089

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	7.7
DANN	Benign	0.94
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;