1-52607655-G-C

Variant names:

• chr1-52607655-G-C
• rs946154
• NM_015696.5:c.401-607G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015696.5(GPX7):​c.401-607G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,026 control chromosomes in the GnomAD database, including 32,935 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 0.66 (32935 hom., cov: 32)
• Consequence: GPX7 NM_015696.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689
• Publications: 11 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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPX7	NM_015696.5	c.401-607G>C		intron_variant	Intron 2 of 2	ENST00000361314.5	NP_056511.2
GPX7	XM_047418560.1	c.293-607G>C		intron_variant	Intron 2 of 2		XP_047274516.1
GPX7	XM_047418564.1	c.272-607G>C		intron_variant	Intron 2 of 2		XP_047274520.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPX7	ENST00000361314.5	c.401-607G>C		intron_variant	Intron 2 of 2	1	NM_015696.5	ENSP00000354677.4
GPX7	ENST00000459779.1	n.*247G>C		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99760 AN: 151908 Hom.: 32902 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.657 AC: 99844 AN: 152026 Hom.: 32935 Cov.: 32 AF XY: 0.661 AC XY: 49090 AN XY: 74314

African (AFR) AF: 0.590 AC: 24432 AN: 41440

American (AMR) AF: 0.713 AC: 10898 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2469 AN: 3468

East Asian (EAS) AF: 0.796 AC: 4125 AN: 5180

South Asian (SAS) AF: 0.773 AC: 3725 AN: 4818

European-Finnish (FIN) AF: 0.677 AC: 7159 AN: 10570

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44933 AN: 67958

Other (OTH) AF: 0.662 AC: 1392 AN: 2102

Alfa AF: 0.666 Hom.: 4156

Bravo AF: 0.656

Asia WGS AF: 0.804 AC: 2797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.7
DANN	Benign	0.88
PhyloP100		-0.69
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: rs946154; hg19: chr1-53073327;