rs7995026

chr13-43279414-A-Cchr13-43279414-A-T

Variant summary

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

The NM_001347969.2(ENOX1):c.1447-9837T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,104 control chromosomes in the GnomAD database, including 2,809 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 0.17 (2809 hom., cov: 32)
• Consequence: ENOX1 NM_001347969.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENOX1	NM_001347969.2	c.1447-9837T>G		intron_variant		ENST00000690772.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENOX1	ENST00000690772.1	c.1447-9837T>G		intron_variant			NM_001347969.2	P1
ENOX1	ENST00000261488.10	c.1447-9837T>G		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25607 AN: 151986 Hom.: 2807 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.168 AC: 25623 AN: 152104 Hom.: 2809 Cov.: 32 AF XY: 0.172 AC XY: 12780 AN XY: 74330

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.172

Alfa AF: 0.135 Hom.: 756

Bravo AF: 0.185

Asia WGS AF: 0.330 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	5.3
Dann	Benign	0.41

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: rs7995026; hg19: chr13-43853550;