Genetic Variant GPX7:p.Phe79Phe (chr1-52606782-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_015696.5(GPX7):c.237T>C(p.Phe79Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 1,614,090 control chromosomes in the GnomAD database, including 567,730 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 0.87 ( 58010 hom., cov: 32)

Exomes 𝑓: 0.83 ( 509720 hom. )

Consequence

GPX7
NM_015696.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53

Publications

22 publications found

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 was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP7

Synonymous conserved (PhyloP=1.53 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPX7	NM_015696.5 link	c.237T>C	p.Phe79Phe	synonymous_variant	Exon 2 of 3	ENST00000361314.5	NP_056511.2	Q96SL4
GPX7	XM_047418560.1 link	c.129T>C	p.Phe43Phe	synonymous_variant	Exon 2 of 3		XP_047274516.1
GPX7	XM_047418564.1 link	c.108T>C	p.Phe36Phe	synonymous_variant	Exon 2 of 3		XP_047274520.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPX7	ENST00000361314.5 link	c.237T>C	p.Phe79Phe	synonymous_variant	Exon 2 of 3	1	NM_015696.5	ENSP00000354677.4		Q96SL4
GPX7	ENST00000459779.1 link	n.247T>C		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.871

AC:

132537

AN:

152100

Hom.:

57961

Cov.:

show subpopulations

Gnomad AFR

AF:

0.956

Gnomad AMI

AF:

0.707

Gnomad AMR

AF:

0.877

Gnomad ASJ

AF:

0.860

Gnomad EAS

AF:

0.797

Gnomad SAS

AF:

0.858

Gnomad FIN

AF:

0.850

Gnomad MID

AF:

0.899

Gnomad NFE

AF:

0.831

Gnomad OTH

AF:

0.864

GnomAD2 exomes

AF:

0.847

AC:

213053

AN:

251468

AF XY:

0.845

show subpopulations

Gnomad AFR exome

AF:

0.958

Gnomad AMR exome

AF:

0.862

Gnomad ASJ exome

AF:

0.865

Gnomad EAS exome

AF:

0.789

Gnomad FIN exome

AF:

0.847

Gnomad NFE exome

AF:

0.830

Gnomad OTH exome

AF:

0.853

GnomAD4 exome

AF:

0.835

AC:

1220070

AN:

1461872

Hom.:

509720

Cov.:

AF XY:

0.835

AC XY:

607151

AN XY:

727242

show subpopulations

African (AFR)

AF:

0.960

AC:

32152

AN:

33480

American (AMR)

AF:

0.864

AC:

38638

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.867

AC:

22648

AN:

26136

East Asian (EAS)

AF:

0.823

AC:

32687

AN:

39700

South Asian (SAS)

AF:

0.859

AC:

74116

AN:

86258

European-Finnish (FIN)

AF:

0.852

AC:

45491

AN:

53418

Middle Eastern (MID)

AF:

0.875

AC:

5048

AN:

5768

European-Non Finnish (NFE)

AF:

0.826

AC:

918233

AN:

1111992

Other (OTH)

AF:

0.845

AC:

51057

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

13373

26746

40118

53491

66864

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21018

42036

63054

84072

105090

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.871

AC:

132643

AN:

152218

Hom.:

58010

Cov.:

AF XY:

0.871

AC XY:

64815

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.956

AC:

39727

AN:

41556

American (AMR)

AF:

0.877

AC:

13414

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.860

AC:

2983

AN:

3470

East Asian (EAS)

AF:

0.798

AC:

4124

AN:

5170

South Asian (SAS)

AF:

0.857

AC:

4134

AN:

4826

European-Finnish (FIN)

AF:

0.850

AC:

9007

AN:

10596

Middle Eastern (MID)

AF:

0.895

AC:

263

AN:

294

European-Non Finnish (NFE)

AF:

0.831

AC:

56526

AN:

67996

Other (OTH)

AF:

0.863

AC:

1820

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

884

1768

2651

3535

4419

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

892

1784

2676

3568

4460

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.847

Hom.:

101032

Bravo

AF:

0.875

Asia WGS

AF:

0.867

AC:

3017

AN:

3478

EpiCase

AF:

0.835

EpiControl

AF:

0.831

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

(source)

DANN

Benign

0.61

PhyloP100

1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over