Variant chr1-52608860-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000361314.5(GPX7):c.*435C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,804 control chromosomes in the GnomAD database, including 20,858 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 0.51 ( 20744 hom., cov: 33)

Exomes 𝑓: 0.54 ( 114 hom. )

Consequence

GPX7
ENST00000361314.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0440

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
GPX7	NM_015696.5 linkuse as main transcript	c.*435C>A	3_prime_UTR_variant	3/3	ENST00000361314.5	NP_056511.2
GPX7	XM_047418560.1 linkuse as main transcript	c.*435C>A	3_prime_UTR_variant	3/3		XP_047274516.1
GPX7	XM_047418564.1 linkuse as main transcript	c.*435C>A	3_prime_UTR_variant	3/3		XP_047274520.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPX7	ENST00000361314.5 linkuse as main transcript	c.*435C>A		3_prime_UTR_variant	3/3	1	NM_015696.5	ENSP00000354677	P1

Frequencies

GnomAD3 genomes

AF:

0.513

AC:

77903

AN:

151894

Hom.:

20736

Cov.:

show subpopulations

Gnomad AFR

AF:

0.355

Gnomad AMI

AF:

0.433

Gnomad AMR

AF:

0.623

Gnomad ASJ

AF:

0.597

Gnomad EAS

AF:

0.764

Gnomad SAS

AF:

0.641

Gnomad FIN

AF:

0.572

Gnomad MID

AF:

0.627

Gnomad NFE

AF:

0.542

Gnomad OTH

AF:

0.550

GnomAD4 exome

AF:

0.539

AC:

427

AN:

792

Hom.:

114

Cov.:

AF XY:

0.510

AC XY:

211

AN XY:

414

show subpopulations

Gnomad4 AFR exome

AF:

0.375

Gnomad4 AMR exome

AF:

0.667

Gnomad4 ASJ exome

AF:

0.643

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.700

Gnomad4 FIN exome

AF:

0.562

Gnomad4 NFE exome

AF:

0.518

Gnomad4 OTH exome

AF:

0.292

GnomAD4 genome

AF:

0.513

AC:

77928

AN:

152012

Hom.:

20744

Cov.:

AF XY:

0.519

AC XY:

38586

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.355

Gnomad4 AMR

AF:

0.623

Gnomad4 ASJ

AF:

0.597

Gnomad4 EAS

AF:

0.764

Gnomad4 SAS

AF:

0.640

Gnomad4 FIN

AF:

0.572

Gnomad4 NFE

AF:

0.542

Gnomad4 OTH

AF:

0.552

Alfa

AF:

0.542

Hom.:

36321

Bravo

AF:

0.511

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

4.4

DANN

Benign

0.71

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