Genetic Variant GPX7:c.401-607G>C (chr1-52607655-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.689

Variant links:

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]

GPX7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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	Effect	Exon rank	MANE	Protein	UniProt
GPX7	NM_015696.5 link	c.401-607G>C	intron_variant	Intron 2 of 2	ENST00000361314.5	NP_056511.2	Q96SL4
GPX7	XM_047418560.1 link	c.293-607G>C	intron_variant	Intron 2 of 2		XP_047274516.1
GPX7	XM_047418564.1 link	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 link	c.401-607G>C		intron_variant	Intron 2 of 2	1	NM_015696.5	ENSP00000354677.4		Q96SL4
GPX7	ENST00000459779.1 link	n.*247G>C		downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.657

AC:

99760

AN:

151908

Hom.:

32902

Cov.:

show subpopulations

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.:

AF XY:

0.661

AC XY:

49090

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.590

Gnomad4 AMR

AF:

0.713

Gnomad4 ASJ

AF:

0.712

Gnomad4 EAS

AF:

0.796

Gnomad4 SAS

AF:

0.773

Gnomad4 FIN

AF:

0.677

Gnomad4 NFE

AF:

0.661

Gnomad4 OTH

AF:

0.662

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

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over