rs4365239

chr15-68952341-C-T

Variant summary

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

The NM_001184780.2(NOX5):c.29+21624C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,166 control chromosomes in the GnomAD database, including 1,446 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 0.11 (1446 hom., cov: 32)
• Consequence: NOX5 NM_001184780.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

Genes affected

NOX5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOX5	NM_001184780.2	c.29+21624C>T		intron_variant
NOX5	NR_033671.3	n.193+21624C>T		intron_variant, non_coding_transcript_variant
NOX5	NR_033672.2	n.193+21624C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17431 AN: 152046 Hom.: 1437 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0804

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0605

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.115 AC: 17468 AN: 152166 Hom.: 1446 Cov.: 32 AF XY: 0.116 AC XY: 8643 AN XY: 74380

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.0635

Gnomad4 ASJ AF: 0.0562

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0804

Gnomad4 NFE AF: 0.0605

Gnomad4 OTH AF: 0.0947

Alfa AF: 0.0677 Hom.: 447

Bravo AF: 0.118

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.4
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4365239; hg19: chr15-69244680;