rs2239585

Variant names:

• chr4-24792697-G-A
• rs2239585
• ENST00000598411.1:c.-17+2595G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-24792697-G-A
• chr4-24792697-G-C

Variant summary

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

The ENST00000598411.1(SOD3):​c.-17+2595G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 151,998 control chromosomes in the GnomAD database, including 2,194 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 0.15 (2194 hom., cov: 32)
• Consequence: SOD3 ENST00000598411.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000598411.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOD3	ENST00000598411.1	TSL:5	c.-17+2595G>A		intron	N/A	ENSP00000472134.1	M0R1V4

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23441 AN: 151882 Hom.: 2188 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0918

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.154 AC: 23478 AN: 151998 Hom.: 2194 Cov.: 32 AF XY: 0.158 AC XY: 11709 AN XY: 74284

African (AFR) AF: 0.245 AC: 10132 AN: 41402

American (AMR) AF: 0.211 AC: 3218 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3470

East Asian (EAS) AF: 0.142 AC: 733 AN: 5162

South Asian (SAS) AF: 0.222 AC: 1070 AN: 4818

European-Finnish (FIN) AF: 0.108 AC: 1141 AN: 10570

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0918 AC: 6242 AN: 67976

Other (OTH) AF: 0.140 AC: 297 AN: 2114

Alfa AF: 0.107 Hom.: 1466

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.59
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2239585; hg19: chr4-24794319;