Genetic Variant NM_015696.5:c.237T>C (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:

Genome browser will be placed here

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015696.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPX7	NM_015696.5	MANE Select	c.237T>C	p.Phe79Phe	synonymous	Exon 2 of 3	NP_056511.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPX7	ENST00000361314.5	TSL:1 MANE Select	c.237T>C	p.Phe79Phe	synonymous	Exon 2 of 3	ENSP00000354677.4
	GPX7	ENST00000459779.1	TSL:2	n.247T>C		non_coding_transcript_exon	Exon 2 of 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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over