dbSNP rs34990910: NOX5:c.1504+52G>A (chr15-69039041-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024505.4(NOX5):c.1504+52G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.042 in 1,595,492 control chromosomes in the GnomAD database, including 2,803 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 0.062 ( 481 hom., cov: 31)

Exomes 𝑓: 0.040 ( 2322 hom. )

Consequence

NOX5
NM_024505.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.19

Publications

4 publications found

Variant links:

Genes affected

NOX5 (HGNC:14874): (NADPH oxidase 5) This gene is predominantly expressed in the testis and lymphocyte-rich areas of spleen and lymph nodes. It encodes a calcium-dependen NADPH oxidase that generates superoxide, and functions as a calcium-dependent proton channel that may regulate redox-dependent processes in lymphocytes and spermatozoa. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Oct 2011]

NOX5 links:

SPESP1-NOX5 (HGNC:):

SPESP1-NOX5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOX5	NM_024505.4 link	c.1504+52G>A		intron_variant	Intron 9 of 15	ENST00000388866.8	NP_078781.3	Q96PH1-1A3QRJ0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOX5	ENST00000388866.8 link	c.1504+52G>A		intron_variant	Intron 9 of 15	1	NM_024505.4	ENSP00000373518.3		Q96PH1-1
SPESP1-NOX5	ENST00000703585.1 link	c.1399+52G>A		intron_variant	Intron 9 of 15			ENSP00000515387.1		Q96PH1-6

Frequencies

GnomAD3 genomes

AF:

0.0620

AC:

9421

AN:

152058

Hom.:

478

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0395

Gnomad ASJ

AF:

0.0185

Gnomad EAS

AF:

0.222

Gnomad SAS

AF:

0.0797

Gnomad FIN

AF:

0.0286

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0315

Gnomad OTH

AF:

0.0549

GnomAD2 exomes

AF:

0.0562

AC:

13994

AN:

249026

AF XY:

0.0547

show subpopulations

Gnomad AFR exome

AF:

0.116

Gnomad AMR exome

AF:

0.0424

Gnomad ASJ exome

AF:

0.0176

Gnomad EAS exome

AF:

0.222

Gnomad FIN exome

AF:

0.0306

Gnomad NFE exome

AF:

0.0284

Gnomad OTH exome

AF:

0.0391

GnomAD4 exome

AF:

0.0399

AC:

57582

AN:

1443316

Hom.:

2322

Cov.:

AF XY:

0.0402

AC XY:

28938

AN XY:

718978

show subpopulations

African (AFR)

AF:

0.123

AC:

4072

AN:

33114

American (AMR)

AF:

0.0429

AC:

1913

AN:

44612

Ashkenazi Jewish (ASJ)

AF:

0.0179

AC:

465

AN:

25938

East Asian (EAS)

AF:

0.230

AC:

9087

AN:

39588

South Asian (SAS)

AF:

0.0744

AC:

6379

AN:

85762

European-Finnish (FIN)

AF:

0.0276

AC:

1421

AN:

51502

Middle Eastern (MID)

AF:

0.0183

AC:

105

AN:

5736

European-Non Finnish (NFE)

AF:

0.0286

AC:

31340

AN:

1097328

Other (OTH)

AF:

0.0469

AC:

2800

AN:

59736

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

2778

5556

8334

11112

13890

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1388

2776

4164

5552

6940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0620

AC:

9433

AN:

152176

Hom.:

481

Cov.:

AF XY:

0.0622

AC XY:

4627

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.112

AC:

4647

AN:

41482

American (AMR)

AF:

0.0396

AC:

606

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0185

AC:

AN:

3466

East Asian (EAS)

AF:

0.222

AC:

1146

AN:

5172

South Asian (SAS)

AF:

0.0797

AC:

384

AN:

4816

European-Finnish (FIN)

AF:

0.0286

AC:

304

AN:

10612

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0315

AC:

2145

AN:

68016

Other (OTH)

AF:

0.0548

AC:

116

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

431

862

1293

1724

2155

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0286

Hom.:

Bravo

AF:

0.0657

Asia WGS

AF:

0.140

AC:

485

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.081

(source)

DANN

Benign

0.65

PhyloP100

-2.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over