chr11-34463426-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001752.4(CAT):​c.1196-679T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,052 control chromosomes in the GnomAD database, including 5,892 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 0.27 ( 5892 hom., cov: 32)

Consequence

CAT
NM_001752.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.38
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
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CATNM_001752.4 linkc.1196-679T>C intron_variant ENST00000241052.5 NP_001743.1 P04040A0A384P5Q0

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CATENST00000241052.5 linkc.1196-679T>C intron_variant 1 NM_001752.4 ENSP00000241052.4 P04040
CATENST00000530343.1 linkn.658-679T>C intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.269
AC:
40890
AN:
151934
Hom.:
5878
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.314
Gnomad AMI
AF:
0.357
Gnomad AMR
AF:
0.317
Gnomad ASJ
AF:
0.245
Gnomad EAS
AF:
0.487
Gnomad SAS
AF:
0.221
Gnomad FIN
AF:
0.196
Gnomad MID
AF:
0.326
Gnomad NFE
AF:
0.228
Gnomad OTH
AF:
0.295
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.269
AC:
40945
AN:
152052
Hom.:
5892
Cov.:
32
AF XY:
0.270
AC XY:
20079
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.314
Gnomad4 AMR
AF:
0.318
Gnomad4 ASJ
AF:
0.245
Gnomad4 EAS
AF:
0.487
Gnomad4 SAS
AF:
0.221
Gnomad4 FIN
AF:
0.196
Gnomad4 NFE
AF:
0.228
Gnomad4 OTH
AF:
0.298
Alfa
AF:
0.243
Hom.:
7922
Bravo
AF:
0.285
Asia WGS
AF:
0.353
AC:
1228
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.14
DANN
Benign
0.32

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs2284365; hg19: chr11-34484973; API