rs4827881

Variant names:

• chrX-100874684-C-A
• rs4827881
• ENST00000865282.1:c.-430G>T

Your query was ambiguous. Multiple possible variants found:

• chrX-100874684-C-A
• chrX-100874684-C-T

Variant summary

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

The ENST00000865282.1(NOX1):​c.-430G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 111,025 control chromosomes in the GnomAD database, including 1,890 homozygotes. There are 7,013 hemizygotes in GnomAD. 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 0.21 (1890 hom., 7013 hem., cov: 23)
• Consequence: NOX1 ENST00000865282.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 2 publications found

Genes affected

NOX1 (HGNC:7889): (NADPH oxidase 1) This gene encodes a member of the NADPH oxidase family of enzymes responsible for the catalytic one-electron transfer of oxygen to generate superoxide or hydrogen peroxide. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000865282.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOX1	ENST00000865282.1		c.-430G>T		upstream_gene	N/A	ENSP00000535341.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 23262 AN: 110970 Hom.: 1889 Cov.: 23

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0914

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.219

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.210 AC: 23283 AN: 111025 Hom.: 1890 Cov.: 23 AF XY: 0.211 AC XY: 7013 AN XY: 33269

African (AFR) AF: 0.129 AC: 3965 AN: 30624

American (AMR) AF: 0.231 AC: 2397 AN: 10394

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 632 AN: 2625

East Asian (EAS) AF: 0.0911 AC: 320 AN: 3511

South Asian (SAS) AF: 0.145 AC: 382 AN: 2636

European-Finnish (FIN) AF: 0.337 AC: 1974 AN: 5865

Middle Eastern (MID) AF: 0.208 AC: 44 AN: 212

European-Non Finnish (NFE) AF: 0.248 AC: 13129 AN: 52963

Other (OTH) AF: 0.215 AC: 326 AN: 1519

Alfa AF: 0.222 Hom.: 19671

Bravo AF: 0.201

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.70
PhyloP100		-0.16
PromoterAI		0.045	Neutral

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4827881;

hg19: chrX-100129673;