rs2036343

Positions:

• chr15-69013422-A-C
• chr15-69013422-A-G

Variant summary

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

The NM_001184780.2(NOX5):​c.30-13106A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0654 in 152,296 control chromosomes in the GnomAD database, including 394 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 0.065 (394 hom., cov: 33)
• Consequence: NOX5 NM_001184780.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75

Genes affected

NOX5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NOX5	NM_001184780.2	c.30-13106A>C		intron_variant			NP_001171709.1
NOX5	NR_033671.3	n.298-13106A>C		intron_variant, non_coding_transcript_variant
NOX5	NR_033672.2	n.298-13106A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0654 AC: 9955 AN: 152178 Hom.: 394 Cov.: 33

Gnomad AFR AF: 0.0857

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0581

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0504

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0654 AC: 9961 AN: 152296 Hom.: 394 Cov.: 33 AF XY: 0.0660 AC XY: 4917 AN XY: 74460

Gnomad4 AFR AF: 0.0856

Gnomad4 AMR AF: 0.0431

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.0928

Gnomad4 FIN AF: 0.0581

Gnomad4 NFE AF: 0.0504

Gnomad4 OTH AF: 0.0573

Alfa AF: 0.0566 Hom.: 23

Bravo AF: 0.0646

Asia WGS AF: 0.127 AC: 440 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	9.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2036343; hg19: chr15-69305761;