chr11-34438994-T-C

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

2

Clinical Significance

Benign no assertion criteria provided B:1

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]

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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 UniProt
CATNM_001752.4 linkuse as main transcriptc.-20T>C 5_prime_UTR_variant 1/13 ENST00000241052.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CATENST00000241052.5 linkuse as main transcriptc.-20T>C 5_prime_UTR_variant 1/131 NM_001752.4 P1

Frequencies

GnomAD3 genomes
AF:
0.603
AC:
91687
AN:
152012
Hom.:
28263
Cov.:
34
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.:
37
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.:
34
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:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, no assertion criteria providedclinical testingMayo Clinic Laboratories, Mayo ClinicOct 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.

Other links and lift over

dbSNP: rs1049982; hg19: chr11-34460541; COSMIC: COSV53810526; API