NM_001347969.2:c.1447-9837T>G

Variant names:

• chr13-43279414-A-C
• rs7995026
• NM_001347969.2:c.1447-9837T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ENOX1	NM_001347969.2	c.1447-9837T>G		intron_variant	Intron 12 of 16	ENST00000690772.1	NP_001334898.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENOX1	ENST00000690772.1	c.1447-9837T>G		intron_variant	Intron 12 of 16		NM_001347969.2	ENSP00000509229.1
ENOX1	ENST00000261488.10	c.1447-9837T>G		intron_variant	Intron 12 of 16	1		ENSP00000261488.6

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

African (AFR) AF: 0.176 AC: 7326 AN: 41518

American (AMR) AF: 0.242 AC: 3688 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3466

East Asian (EAS) AF: 0.604 AC: 3107 AN: 5144

South Asian (SAS) AF: 0.167 AC: 805 AN: 4806

European-Finnish (FIN) AF: 0.118 AC: 1252 AN: 10594

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8460 AN: 67990

Other (OTH) AF: 0.172 AC: 364 AN: 2112

Alfa AF: 0.134 Hom.: 846

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
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7995026; hg19: chr13-43853550;