rs1369953

chr11-89548817-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000528319.1(ENSG00000255429):n.173-2122G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,022 control chromosomes in the GnomAD database, including 9,871 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 0.36 (9871 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENST00000528319.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOX4	NM_001143837.2	c.-364-2122G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000528319.1	n.173-2122G>C		intron_variant, non_coding_transcript_variant		5
	ENST00000624036.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54330 AN: 151900 Hom.: 9859 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.360

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.358 AC: 54380 AN: 152022 Hom.: 9871 Cov.: 32 AF XY: 0.349 AC XY: 25906 AN XY: 74298

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.367

Alfa AF: 0.376 Hom.: 1317

Bravo AF: 0.360

Asia WGS AF: 0.374 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1369953; hg19: chr11-89281985;