6-155434270-A-G

Variant names:

• chr6-155434270-A-G
• rs231958
• NM_015718.3:c.798+2148T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015718.3(NOX3):​c.798+2148T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,028 control chromosomes in the GnomAD database, including 14,399 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 0.43 (14399 hom., cov: 32)
• Consequence: NOX3 NM_015718.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.988
• Publications: 7 publications found

Genes affected

NOX3 (HGNC:7890): (NADPH oxidase 3) This gene encodes a member of the NOX family of NADPH oxidases. These enzymes have the capacity to generate superoxide and other reactive oxygen species (ROS) and transport electrons across the plasma membrane. The ROS generated by family members have been implicated in numerous biological functions including host defense, posttranlational processing of proteins, cellular signaling, regulation of gene expression, and cell differentiation. The protein encoded by this gene is expressed predominantly in the inner ear and is involved in the biogenesis of otoconia/otolith, which are crystalline structures of the inner ear involved in the perception of gravity.[provided by RefSeq, May 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015718.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOX3	NM_015718.3	MANE Select	c.798+2148T>C		intron	N/A	NP_056533.1	Q9HBY0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOX3	ENST00000159060.3	TSL:1 MANE Select	c.798+2148T>C		intron	N/A	ENSP00000159060.2	Q9HBY0

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64563 AN: 151910 Hom.: 14373 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.425 AC: 64622 AN: 152028 Hom.: 14399 Cov.: 32 AF XY: 0.431 AC XY: 32024 AN XY: 74304

African (AFR) AF: 0.525 AC: 21741 AN: 41442

American (AMR) AF: 0.312 AC: 4775 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3468

East Asian (EAS) AF: 0.589 AC: 3050 AN: 5174

South Asian (SAS) AF: 0.405 AC: 1952 AN: 4820

European-Finnish (FIN) AF: 0.541 AC: 5714 AN: 10556

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.361 AC: 24521 AN: 67972

Other (OTH) AF: 0.396 AC: 835 AN: 2110

Alfa AF: 0.375 Hom.: 49478

Bravo AF: 0.413

Asia WGS AF: 0.503 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.50
PhyloP100		0.99
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs231958; hg19: chr6-155755404; COSMIC: COSV50161789;