rs17538444

chr13-43260134-C-T

Variant summary

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

The NM_001347969.2(ENOX1):c.1611+5264G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,296 control chromosomes in the GnomAD database, including 236 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 0.051 (236 hom., cov: 32)
• Consequence: ENOX1 NM_001347969.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

Genes affected

ENOX1 (HGNC:25474): (ecto-NOX disulfide-thiol exchanger 1) The protein encoded by this gene is involved in plasma membrane electron transport pathways. The encoded protein has both a hydroquinone (NADH) oxidase activity and a protein disulfide-thiol interchange activity. The two activities cycle with a periodicity of 24 minutes, with one activity being at its peak when the other is at its lowest. [provided by RefSeq, Dec 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.064 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENOX1	NM_001347969.2	c.1611+5264G>A		intron_variant		ENST00000690772.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENOX1	ENST00000690772.1	c.1611+5264G>A		intron_variant			NM_001347969.2	P1
ENOX1	ENST00000261488.10	c.1611+5264G>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.0509 AC: 7749 AN: 152178 Hom.: 236 Cov.: 32

Gnomad AFR AF: 0.0381

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.0492

Gnomad FIN AF: 0.0523

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0656

Gnomad OTH AF: 0.0530

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

GnomAD4 genome AF: 0.0509 AC: 7752 AN: 152296 Hom.: 236 Cov.: 32 AF XY: 0.0500 AC XY: 3721 AN XY: 74476

Gnomad4 AFR AF: 0.0381

Gnomad4 AMR AF: 0.0351

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0501

Gnomad4 FIN AF: 0.0523

Gnomad4 NFE AF: 0.0656

Gnomad4 OTH AF: 0.0525

Alfa AF: 0.0612 Hom.: 187

Bravo AF: 0.0482

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.7
Dann	Benign	0.74

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

Publications

LitVar

Other links and lift over

dbSNP: rs17538444; hg19: chr13-43834270;