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GeneBe

11-34461361-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

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 (no stars).

Frequency

Genomes: 𝑓 0.23 ( 4283 hom., cov: 32)
Exomes 𝑓: 0.23 ( 41310 hom. )

Consequence

CAT
NM_001752.4 synonymous

Scores

2

Clinical Significance

Benign no assertion criteria provided B:1

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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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 no_assertion_criteria_provided, 0 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.503 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
CATNM_001752.4 linkuse as main transcriptc.1167C>T p.Asp389= synonymous_variant 9/13 ENST00000241052.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CATENST00000241052.5 linkuse as main transcriptc.1167C>T p.Asp389= synonymous_variant 9/131 NM_001752.4 P1
CATENST00000530343.1 linkuse as main transcriptn.629C>T non_coding_transcript_exon_variant 1/22
CATENST00000650153.1 linkuse as main transcriptc.*1059C>T 3_prime_UTR_variant, NMD_transcript_variant 9/9

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.225
AC:
34219
AN:
152006
Hom.:
4273
Cov.:
32
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.:
34
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.225
AC:
34254
AN:
152124
Hom.:
4283
Cov.:
32
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: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
-0.28
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.

Other links and lift over

dbSNP: rs769217; hg19: chr11-34482908; COSMIC: COSV53811275; COSMIC: COSV53811275; API