Variant rs5746112 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000636.4(SOD2):c.227-275_227-271del 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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SOD2	NM_000636.4 linkuse as main transcript	c.227-275_227-271del		intron_variant		ENST00000538183.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOD2	ENST00000538183.7 linkuse as main transcript	c.227-275_227-271del		intron_variant		1	NM_000636.4	P1	P04179-1

Frequencies

GnomAD3 genomes

AF:

0.429

AC:

64918

AN:

151272

Hom.:

14547

Cov.:

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.:

AF XY:

0.425

AC XY:

31433

AN XY:

73936

show subpopulations

Gnomad4 AFR

AF:

0.320

Gnomad4 AMR

AF:

0.495

Gnomad4 ASJ

AF:

0.476

Gnomad4 EAS

AF:

0.132

Gnomad4 SAS

AF:

0.475

Gnomad4 FIN

AF:

0.460

Gnomad4 NFE

AF:

0.492

Gnomad4 OTH

AF:

0.436

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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over