Variant 11-34461361-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_001752.4(CAT):c.1167C>T(p.Asp389=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,613,666 control chromosomes in the GnomAD database, including 45,593 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.23 ( 4283 hom., cov: 32)

Exomes 𝑓: 0.23 ( 41310 hom. )

Consequence

CAT
NM_001752.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -0.503

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BP6

Variant 11-34461361-C-T is Benign according to our data. Variant chr11-34461361-C-T is described in ClinVar as [Benign]. Clinvar id is 559061.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.503 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 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.1167C>T	p.Asp389=	synonymous_variant	9/13	ENST00000241052.5	NP_001743.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
CAT	ENST00000241052.5 linkuse as main transcript	c.1167C>T	p.Asp389=	synonymous_variant	9/13	1	NM_001752.4	ENSP00000241052	P1
CAT	ENST00000530343.1 linkuse as main transcript	n.629C>T		non_coding_transcript_exon_variant	1/2	2
CAT	ENST00000650153.1 linkuse as main transcript	c.*1059C>T		3_prime_UTR_variant, NMD_transcript_variant	9/9			ENSP00000497751

Frequencies

GnomAD3 genomes

AF:

0.225

AC:

34219

AN:

152006

Hom.:

4273

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.304

Gnomad ASJ

AF:

0.245

Gnomad EAS

AF:

0.476

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.227

Gnomad OTH

AF:

0.268

GnomAD3 exomes

AF:

0.249

AC:

62637

AN:

251478

Hom.:

8496

AF XY:

0.249

AC XY:

33838

AN XY:

135914

show subpopulations

Gnomad AFR exome

AF:

0.160

Gnomad AMR exome

AF:

0.297

Gnomad ASJ exome

AF:

0.241

Gnomad EAS exome

AF:

0.464

Gnomad SAS exome

AF:

0.238

Gnomad FIN exome

AF:

0.205

Gnomad NFE exome

AF:

0.224

Gnomad OTH exome

AF:

0.266

GnomAD4 exome

AF:

0.232

AC:

339031

AN:

1461542

Hom.:

41310

Cov.:

AF XY:

0.234

AC XY:

169792

AN XY:

727076

show subpopulations

Gnomad4 AFR exome

AF:

0.161

Gnomad4 AMR exome

AF:

0.296

Gnomad4 ASJ exome

AF:

0.243

Gnomad4 EAS exome

AF:

0.452

Gnomad4 SAS exome

AF:

0.238

Gnomad4 FIN exome

AF:

0.203

Gnomad4 NFE exome

AF:

0.223

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.225

AC:

34254

AN:

152124

Hom.:

4283

Cov.:

AF XY:

0.227

AC XY:

16896

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.161

Gnomad4 AMR

AF:

0.305

Gnomad4 ASJ

AF:

0.245

Gnomad4 EAS

AF:

0.476

Gnomad4 SAS

AF:

0.220

Gnomad4 FIN

AF:

0.197

Gnomad4 NFE

AF:

0.227

Gnomad4 OTH

AF:

0.271

Alfa

AF:

0.234

Hom.:

8699

Bravo

AF:

0.234

Asia WGS

AF:

0.339

AC:

1177

AN:

3478

EpiCase

AF:

0.239

EpiControl

AF:

0.238

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

-0.28

CADD

Benign

2.2

DANN

Benign

0.69

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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