4-24796575-A-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_003102.4(SOD3):c.-17+924A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.000021 ( 0 hom., cov: 24)
Failed GnomAD Quality Control
Consequence
SOD3
NM_003102.4 intron
NM_003102.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.553
Publications
0 publications found
Genes affected
SOD3 (HGNC:11181): (superoxide dismutase 3) This gene encodes a member of the superoxide dismutase (SOD) protein family. SODs are antioxidant enzymes that catalyze the conversion of superoxide radicals into hydrogen peroxide and oxygen, which may protect the brain, lungs, and other tissues from oxidative stress. Proteolytic processing of the encoded protein results in the formation of two distinct homotetramers that differ in their ability to interact with the extracellular matrix (ECM). Homotetramers consisting of the intact protein, or type C subunit, exhibit high affinity for heparin and are anchored to the ECM. Homotetramers consisting of a proteolytically cleaved form of the protein, or type A subunit, exhibit low affinity for heparin and do not interact with the ECM. A mutation in this gene may be associated with increased heart disease risk. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.0000206 AC: 3AN: 145568Hom.: 0 Cov.: 24 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
145568
Hom.:
Cov.:
24
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.0000206 AC: 3AN: 145634Hom.: 0 Cov.: 24 AF XY: 0.0000141 AC XY: 1AN XY: 70826 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
3
AN:
145634
Hom.:
Cov.:
24
AF XY:
AC XY:
1
AN XY:
70826
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
2
AN:
38110
American (AMR)
AF:
AC:
1
AN:
14698
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3436
East Asian (EAS)
AF:
AC:
0
AN:
4898
South Asian (SAS)
AF:
AC:
0
AN:
4562
European-Finnish (FIN)
AF:
AC:
0
AN:
9624
Middle Eastern (MID)
AF:
AC:
0
AN:
268
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67132
Other (OTH)
AF:
AC:
0
AN:
2004
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000102688), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.325
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
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0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
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>80
Age
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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