NM_015696.5:c.138+1295C>G

Variant names:

• chr1-52603842-C-G
• rs3753753
• NM_015696.5:c.138+1295C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GPX7	NM_015696.5	c.138+1295C>G		intron_variant	Intron 1 of 2	ENST00000361314.5	NP_056511.2
GPX7	XM_047418564.1	c.-288C>G		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 3		XP_047274520.1
GPX7	XM_047418564.1	c.-288C>G		5_prime_UTR_variant	Exon 1 of 3		XP_047274520.1
GPX7	XM_047418560.1	c.30+247C>G		intron_variant	Intron 1 of 2		XP_047274516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPX7	ENST00000361314.5	c.138+1295C>G		intron_variant	Intron 1 of 2	1	NM_015696.5	ENSP00000354677.4
GPX7	ENST00000459779.1	n.148+1295C>G		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.882 AC: 36600 AN: 41488

American (AMR) AF: 0.790 AC: 12060 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2583 AN: 3470

East Asian (EAS) AF: 0.796 AC: 4114 AN: 5168

South Asian (SAS) AF: 0.808 AC: 3885 AN: 4808

European-Finnish (FIN) AF: 0.760 AC: 8035 AN: 10568

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49357 AN: 67976

Other (OTH) AF: 0.769 AC: 1619 AN: 2106

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
PhyloP100		-0.74
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3753753; hg19: chr1-53069514;