GeneBe

NM_000636.4:c.227-275_227-271delATTTC

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_000636.4(SOD2):​c.227-275_227-271delATTTC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.43 ( 14560 hom., cov: 0)

Consequence

SOD2
NM_000636.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.26

Publications

2 publications found
Variant links:
Genes affected
SOD2 (HGNC:11180): (superoxide dismutase 2) This gene is a member of the iron/manganese superoxide dismutase family. It encodes a mitochondrial protein that forms a homotetramer and binds one manganese ion per subunit. This protein binds to the superoxide byproducts of oxidative phosphorylation and converts them to hydrogen peroxide and diatomic oxygen. Mutations in this gene have been associated with idiopathic cardiomyopathy (IDC), premature aging, sporadic motor neuron disease, and cancer. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 1. [provided by RefSeq, Apr 2016]
SOD2 Gene-Disease associations (from GenCC):
  • cardiomyopathy
    Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SOD2NM_000636.4 linkc.227-275_227-271delATTTC intron_variant Intron 2 of 4 ENST00000538183.7 NP_000627.2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SOD2ENST00000538183.7 linkc.227-275_227-271delATTTC intron_variant Intron 2 of 4 1 NM_000636.4 ENSP00000446252.1 P04179-1

Frequencies

GnomAD3 genomes
AF:
0.429
AC:
64918
AN:
151272
Hom.:
14547
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.320
Gnomad AMI
AF:
0.483
Gnomad AMR
AF:
0.494
Gnomad ASJ
AF:
0.476
Gnomad EAS
AF:
0.132
Gnomad SAS
AF:
0.477
Gnomad FIN
AF:
0.460
Gnomad MID
AF:
0.417
Gnomad NFE
AF:
0.492
Gnomad OTH
AF:
0.440
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.429
AC:
64934
AN:
151392
Hom.:
14560
Cov.:
0
AF XY:
0.425
AC XY:
31433
AN XY:
73936
show subpopulations
African (AFR)
AF:
0.320
AC:
13197
AN:
41302
American (AMR)
AF:
0.495
AC:
7526
AN:
15192
Ashkenazi Jewish (ASJ)
AF:
0.476
AC:
1648
AN:
3460
East Asian (EAS)
AF:
0.132
AC:
684
AN:
5174
South Asian (SAS)
AF:
0.475
AC:
2285
AN:
4806
European-Finnish (FIN)
AF:
0.460
AC:
4813
AN:
10452
Middle Eastern (MID)
AF:
0.404
AC:
118
AN:
292
European-Non Finnish (NFE)
AF:
0.492
AC:
33312
AN:
67712
Other (OTH)
AF:
0.436
AC:
914
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.494
Heterozygous variant carriers
0
1813
3625
5438
7250
9063
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
606
1212
1818
2424
3030
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.474
Hom.:
2106
Bravo
AF:
0.426
Asia WGS
AF:
0.323
AC:
1122
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.3
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs5746112; hg19: chr6-160109544; API