NM_001752.4:c.66+1077C>A

Variant names:

• chr11-34440156-C-A
• rs11032700
• NM_001752.4:c.66+1077C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001752.4(CAT):​c.66+1077C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,036 control chromosomes in the GnomAD database, including 32,698 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 0.65 (32698 hom., cov: 31)
• Consequence: CAT NM_001752.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 16 publications found

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 Gene-Disease associations (from GenCC):

• acatalasia

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAT	NM_001752.4	c.66+1077C>A		intron_variant	Intron 1 of 12	ENST00000241052.5	NP_001743.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAT	ENST00000241052.5	c.66+1077C>A		intron_variant	Intron 1 of 12	1	NM_001752.4	ENSP00000241052.4

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98412 AN: 151918 Hom.: 32680 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.648 AC: 98471 AN: 152036 Hom.: 32698 Cov.: 31 AF XY: 0.641 AC XY: 47649 AN XY: 74294

African (AFR) AF: 0.742 AC: 30761 AN: 41458

American (AMR) AF: 0.524 AC: 8011 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2337 AN: 3468

East Asian (EAS) AF: 0.288 AC: 1488 AN: 5162

South Asian (SAS) AF: 0.631 AC: 3045 AN: 4822

European-Finnish (FIN) AF: 0.577 AC: 6092 AN: 10554

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44750 AN: 67978

Other (OTH) AF: 0.618 AC: 1303 AN: 2110

Alfa AF: 0.656 Hom.: 38855

Bravo AF: 0.644

Asia WGS AF: 0.460 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.3
DANN	Benign	0.61
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11032700; hg19: chr11-34461703;