rs4880

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000636(SOD2):c.47T>C(p.Val16Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151824 control chromosomes in the gnomAD Genomes database, including 17245 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting interpretations of pathogenicity,risk factor (no stars).

Frequency

Genomes: 𝑓 0.47 ( 17245 hom., cov: 32)

Exomes 𝑓: 0.48 ( 29854 hom. )

Consequence

SOD2
NM_000636 missense

Scores

Clinical Significance

Conflicting interpretations of pathogenicity; risk factor no assertion criteria provided P:1B:1O:1

Conservation

PhyloP100: 2.20

Links

SOD2 (HGNC:11180):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=3.9671322E-5).

BA1

GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.526 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.47T>C	p.Val16Ala	missense_variant	2/5	ENST00000538183.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOD2	ENST00000538183.7 linkuse as main transcript	c.47T>C	p.Val16Ala	missense_variant	2/5	1	NM_000636.4	P1	P04179-1

Frequencies

GnomAD3 genomes

AF:

0.470

AC:

71427

AN:

151824

Hom.:

17245

Cov.:

show subpopulations

Gnomad AFR

AF:

0.425

Gnomad AMI

AF:

0.490

Gnomad AMR

AF:

0.536

Gnomad ASJ

AF:

0.519

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.513

Gnomad FIN

AF:

0.467

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.503

Gnomad OTH

AF:

0.474

GnomAD3 exomes

AF:

0.484

AC:

117709

AN:

243226

Hom.:

29854

AF XY:

0.484

AC XY:

63735

AN XY:

131784

show subpopulations

Gnomad AFR exome

AF:

0.425

Gnomad AMR exome

AF:

0.623

Gnomad ASJ exome

AF:

0.513

Gnomad EAS exome

AF:

0.137

Gnomad SAS exome

AF:

0.519

Gnomad FIN exome

AF:

0.472

Gnomad NFE exome

AF:

0.497

Gnomad OTH exome

AF:

0.485

GnomAD4 exome

AF:

0.492

AC:

717843

AN:

1458702

Hom.:

180259

AF XY:

0.491

AC XY:

356365

AN XY:

725526

show subpopulations

Gnomad4 AFR exome

AF:

0.429

Gnomad4 AMR exome

AF:

0.613

Gnomad4 ASJ exome

AF:

0.506

Gnomad4 EAS exome

AF:

0.131

Gnomad4 SAS exome

AF:

0.519

Gnomad4 FIN exome

AF:

0.481

Gnomad4 NFE exome

AF:

0.501

Gnomad4 OTH exome

AF:

0.476

Alfa

AF:

0.488

Hom.:

30554

Bravo

AF:

0.472

TwinsUK

AF:

0.490

AC:

1818

ALSPAC

AF:

0.477

AC:

1839

ESP6500AA

AF:

0.420

AC:

1849

ESP6500EA

AF:

0.500

AC:

4303

ExAC

AF:

0.476

AC:

57687

Asia WGS

AF:

0.349

AC:

1214

AN:

3478

ClinVar

Significance: Conflicting interpretations of pathogenicity; risk factor

Submissions summary: Pathogenic:1Benign:1Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Microvascular complications of diabetes, susceptibility to, 6

Pathogenic:1Other:1

Likely risk allele, no assertion criteria provided	reference population	iDNA Genomics	Jan 01, 2007	- -
risk factor, no assertion criteria provided	literature only	OMIM	Jan 01, 2007	- -

SUPEROXIDE DISMUTASE 2 POLYMORPHISM

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Jan 01, 2007

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.066

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.61

Cadd

Benign

Dann

Benign

0.82

Eigen

Benign

-0.85

Eigen_PC

Benign

-0.81

FATHMM_MKL

Benign

0.13

MetaRNN

Benign

0.000040

T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.93

MutationTaster

Benign

1.0

P;P;P;P;P;P;P

PrimateAI

Uncertain

0.64

PROVEAN

Benign

0.35

N;N;N;N;N;N;N;N

REVEL

Benign

0.048

Sift

Benign

0.93

T;T;T;T;T;T;T;T

Sift4G

Benign

0.98

T;T;T;T;T;.;.;T

Polyphen

0.024

.;.;.;.;.;.;.;B

Vest4

0.034

MPC

0.56

ClinPred

0.0093

GERP RS

3.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.020

gMVP

0.24

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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over