Genetic Variant NOX4P1:n.49349282C>A (chr11-49349282-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant allele was found at a frequency of 0.497 in 151,968 control chromosomes in the GnomAD database, including 21,009 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 0.50 ( 21009 hom., cov: 32)

Consequence

NOX4P1
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0260

Publications

3 publications found

Variant links:

Genes affected

NOX4P1 (HGNC:56735): (NOX4 pseudogene 1)

NOX4P1 links:

ENSG00000294854 (HGNC:):

ENSG00000294854 links:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOX4P1		n.49349282C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOX4P1	ENST00000529674.1 link	n.478-1916C>A		intron_variant	Intron 3 of 7	6
ENSG00000294854	ENST00000726381.1 link	n.234-1920C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.498

AC:

75560

AN:

151852

Hom.:

20997

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.674

Gnomad AMR

AF:

0.620

Gnomad ASJ

AF:

0.717

Gnomad EAS

AF:

0.538

Gnomad SAS

AF:

0.542

Gnomad FIN

AF:

0.579

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.596

Gnomad OTH

AF:

0.557

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

GnomAD4 genome

AF:

0.497

AC:

75578

AN:

151968

Hom.:

21009

Cov.:

AF XY:

0.499

AC XY:

37070

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.232

AC:

9632

AN:

41440

American (AMR)

AF:

0.620

AC:

9466

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.717

AC:

2485

AN:

3466

East Asian (EAS)

AF:

0.539

AC:

2785

AN:

5168

South Asian (SAS)

AF:

0.542

AC:

2610

AN:

4812

European-Finnish (FIN)

AF:

0.579

AC:

6115

AN:

10568

Middle Eastern (MID)

AF:

0.602

AC:

177

AN:

294

European-Non Finnish (NFE)

AF:

0.596

AC:

40512

AN:

67946

Other (OTH)

AF:

0.562

AC:

1184

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1709

3418

5127

6836

8545

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

660

1320

1980

2640

3300

<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:

0.549

Hom.:

8708

Bravo

AF:

0.492

Asia WGS

AF:

0.495

AC:

1721

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.4

(source)

DANN

Benign

0.46

PhyloP100

-0.026

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over