rs3753753

chr1-52603842-C-Gchr1-52603842-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015696.5(GPX7):c.138+1295C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,044 control chromosomes in the GnomAD database, including 46,889 homozygotes. 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 0.78 (46889 hom., cov: 30)
• Consequence: GPX7 NM_015696.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

Genes affected

GPX7 (HGNC:4559): (glutathione peroxidase 7) Enables catalase activity. Predicted to be involved in cellular response to oxidative stress. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPX7	NM_015696.5	c.138+1295C>G		intron_variant		ENST00000361314.5
GPX7	XM_047418564.1	c.-288C>G		5_prime_UTR_variant	1/3
GPX7	XM_047418560.1	c.30+247C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPX7	ENST00000361314.5	c.138+1295C>G		intron_variant		1	NM_015696.5	P1
GPX7	ENST00000459779.1	n.148+1295C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118919 AN: 151926 Hom.: 46856 Cov.: 30

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.768

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.783 AC: 119005 AN: 152044 Hom.: 46889 Cov.: 30 AF XY: 0.784 AC XY: 58276 AN XY: 74328

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.769

Alfa AF: 0.762 Hom.: 5151

Bravo AF: 0.786

Asia WGS AF: 0.837 AC: 2915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	5.5
Dann	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3753753; hg19: chr1-53069514;