chr11-34442192-T-C

Position:

• chr11-34442192-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000241052.5(CAT):​c.66+3113T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,314 control chromosomes in the GnomAD database, including 1,374 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 0.12 (1374 hom., cov: 33)
• Consequence: CAT ENST00000241052.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAT	NM_001752.4	c.66+3113T>C		intron_variant		ENST00000241052.5	NP_001743.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAT	ENST00000241052.5	c.66+3113T>C		intron_variant		1	NM_001752.4	ENSP00000241052	P1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18236 AN: 152196 Hom.: 1365 Cov.: 33

Gnomad AFR AF: 0.0495

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.138

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.120 AC: 18253 AN: 152314 Hom.: 1374 Cov.: 33 AF XY: 0.124 AC XY: 9218 AN XY: 74468

Gnomad4 AFR AF: 0.0493

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.141

Alfa AF: 0.125 Hom.: 389

Bravo AF: 0.123

Asia WGS AF: 0.181 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.92

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

Other links and lift over

dbSNP: rs4756146; hg19: chr11-34463739;