Variant chr11-34438994-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001752.4(CAT):c.-20T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 1,575,640 control chromosomes in the GnomAD database, including 329,145 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.60 ( 28280 hom., cov: 34)

Exomes 𝑓: 0.65 ( 300865 hom. )

Consequence

CAT
NM_001752.4 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.144

Variant links:

Genes affected

CAT (HGNC:1516): (catalase) This gene encodes catalase, a key antioxidant enzyme in the bodies defense against oxidative stress. Catalase is a heme enzyme that is present in the peroxisome of nearly all aerobic cells. Catalase converts the reactive oxygen species hydrogen peroxide to water and oxygen and thereby mitigates the toxic effects of hydrogen peroxide. Oxidative stress is hypothesized to play a role in the development of many chronic or late-onset diseases such as diabetes, asthma, Alzheimer's disease, systemic lupus erythematosus, rheumatoid arthritis, and cancers. Polymorphisms in this gene have been associated with decreases in catalase activity but, to date, acatalasemia is the only disease known to be caused by this gene. [provided by RefSeq, Oct 2009]

CAT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 11-34438994-T-C is Benign according to our data. Variant chr11-34438994-T-C is described in ClinVar as [Benign]. Clinvar id is 559060.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-34438994-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAT	NM_001752.4 linkuse as main transcript	c.-20T>C		5_prime_UTR_variant	1/13	ENST00000241052.5	NP_001743.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAT	ENST00000241052.5 linkuse as main transcript	c.-20T>C		5_prime_UTR_variant	1/13	1	NM_001752.4	ENSP00000241052	P1

Frequencies

GnomAD3 genomes

AF:

0.603

AC:

91687

AN:

152012

Hom.:

28263

Cov.:

show subpopulations

Gnomad AFR

AF:

0.571

Gnomad AMI

AF:

0.543

Gnomad AMR

AF:

0.505

Gnomad ASJ

AF:

0.676

Gnomad EAS

AF:

0.286

Gnomad SAS

AF:

0.633

Gnomad FIN

AF:

0.606

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.664

Gnomad OTH

AF:

0.583

GnomAD3 exomes

AF:

0.589

AC:

113921

AN:

193292

Hom.:

34918

AF XY:

0.600

AC XY:

62625

AN XY:

104392

show subpopulations

Gnomad AFR exome

AF:

0.570

Gnomad AMR exome

AF:

0.450

Gnomad ASJ exome

AF:

0.683

Gnomad EAS exome

AF:

0.285

Gnomad SAS exome

AF:

0.628

Gnomad FIN exome

AF:

0.598

Gnomad NFE exome

AF:

0.670

Gnomad OTH exome

AF:

0.606

GnomAD4 exome

AF:

0.646

AC:

919429

AN:

1423512

Hom.:

300865

Cov.:

AF XY:

0.645

AC XY:

455170

AN XY:

705166

show subpopulations

Gnomad4 AFR exome

AF:

0.571

Gnomad4 AMR exome

AF:

0.456

Gnomad4 ASJ exome

AF:

0.684

Gnomad4 EAS exome

AF:

0.330

Gnomad4 SAS exome

AF:

0.626

Gnomad4 FIN exome

AF:

0.596

Gnomad4 NFE exome

AF:

0.670

Gnomad4 OTH exome

AF:

0.621

GnomAD4 genome

AF:

0.603

AC:

91742

AN:

152128

Hom.:

28280

Cov.:

AF XY:

0.598

AC XY:

44509

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.571

Gnomad4 AMR

AF:

0.504

Gnomad4 ASJ

AF:

0.676

Gnomad4 EAS

AF:

0.287

Gnomad4 SAS

AF:

0.633

Gnomad4 FIN

AF:

0.606

Gnomad4 NFE

AF:

0.664

Gnomad4 OTH

AF:

0.579

Alfa

AF:

0.630

Hom.:

6329

Bravo

AF:

0.589

Asia WGS

AF:

0.451

AC:

1572

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Oct 19, 2015	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.1

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over