Variant 15-69033241-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_024505.4(NOX5):c.819C>T(p.Cys273=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.934 in 1,597,274 control chromosomes in the GnomAD database, including 701,373 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 0.87 ( 58459 hom., cov: 33)

Exomes 𝑓: 0.94 ( 642914 hom. )

Consequence

NOX5
NM_024505.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.280

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BP7

Synonymous conserved (PhyloP=-0.28 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOX5	NM_024505.4 linkuse as main transcript	c.819C>T	p.Cys273=	synonymous_variant	5/16	ENST00000388866.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOX5	ENST00000388866.8 linkuse as main transcript	c.819C>T	p.Cys273=	synonymous_variant	5/16	1	NM_024505.4		Q96PH1-1
NOX5	ENST00000530406.7 linkuse as main transcript	c.735C>T	p.Cys245=	synonymous_variant	5/16	1		P1	Q96PH1-3
NOX5	ENST00000525143.5 linkuse as main transcript	c.219C>T	p.Cys73=	synonymous_variant, NMD_transcript_variant	2/12	1
NOX5	ENST00000527315.5 linkuse as main transcript	n.3975C>T		non_coding_transcript_exon_variant	4/15	2

Frequencies

GnomAD3 genomes

AF:

0.866

AC:

131821

AN:

152154

Hom.:

58438

Cov.:

show subpopulations

Gnomad AFR

AF:

0.670

Gnomad AMI

AF:

0.964

Gnomad AMR

AF:

0.935

Gnomad ASJ

AF:

0.959

Gnomad EAS

AF:

0.752

Gnomad SAS

AF:

0.896

Gnomad FIN

AF:

0.946

Gnomad MID

AF:

0.959

Gnomad NFE

AF:

0.957

Gnomad OTH

AF:

0.898

GnomAD3 exomes

AF:

0.913

AC:

210611

AN:

230634

Hom.:

97073

AF XY:

0.918

AC XY:

116318

AN XY:

126660

show subpopulations

Gnomad AFR exome

AF:

0.665

Gnomad AMR exome

AF:

0.941

Gnomad ASJ exome

AF:

0.964

Gnomad EAS exome

AF:

0.752

Gnomad SAS exome

AF:

0.896

Gnomad FIN exome

AF:

0.949

Gnomad NFE exome

AF:

0.960

Gnomad OTH exome

AF:

0.934

GnomAD4 exome

AF:

0.941

AC:

1360188

AN:

1445002

Hom.:

642914

Cov.:

AF XY:

0.941

AC XY:

676975

AN XY:

719204

show subpopulations

Gnomad4 AFR exome

AF:

0.651

Gnomad4 AMR exome

AF:

0.939

Gnomad4 ASJ exome

AF:

0.962

Gnomad4 EAS exome

AF:

0.750

Gnomad4 SAS exome

AF:

0.897

Gnomad4 FIN exome

AF:

0.950

Gnomad4 NFE exome

AF:

0.960

Gnomad4 OTH exome

AF:

0.925

GnomAD4 genome

AF:

0.866

AC:

131883

AN:

152272

Hom.:

58459

Cov.:

AF XY:

0.866

AC XY:

64516

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.670

Gnomad4 AMR

AF:

0.935

Gnomad4 ASJ

AF:

0.959

Gnomad4 EAS

AF:

0.752

Gnomad4 SAS

AF:

0.895

Gnomad4 FIN

AF:

0.946

Gnomad4 NFE

AF:

0.957

Gnomad4 OTH

AF:

0.897

Alfa

AF:

0.942

Hom.:

67299

Bravo

AF:

0.856

Asia WGS

AF:

0.802

AC:

2790

AN:

3478

EpiCase

AF:

0.961

EpiControl

AF:

0.962

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

5.4

DANN

Benign

0.93

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

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