13-43240100-G-A

Variant names:

• chr13-43240100-G-A
• rs9285151
• NM_001347969.2:c.1612-3362C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001347969.2(ENOX1):​c.1612-3362C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,972 control chromosomes in the GnomAD database, including 20,576 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 0.50 (20576 hom., cov: 32)
• Consequence: ENOX1 NM_001347969.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001347969.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENOX1	NM_001347969.2	MANE Select	c.1612-3362C>T		intron	N/A	NP_001334898.1
	ENOX1	NM_001347963.2		c.1717-3362C>T		intron	N/A	NP_001334892.1
	ENOX1	NM_001127615.3		c.1612-3362C>T		intron	N/A	NP_001121087.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENOX1	ENST00000690772.1	MANE Select	c.1612-3362C>T		intron	N/A	ENSP00000509229.1
	ENOX1	ENST00000261488.10	TSL:1	c.1612-3362C>T		intron	N/A	ENSP00000261488.6

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75401 AN: 151854 Hom.: 20581 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.496 AC: 75411 AN: 151972 Hom.: 20576 Cov.: 32 AF XY: 0.495 AC XY: 36786 AN XY: 74258

African (AFR) AF: 0.259 AC: 10712 AN: 41434

American (AMR) AF: 0.534 AC: 8157 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2145 AN: 3470

East Asian (EAS) AF: 0.525 AC: 2707 AN: 5154

South Asian (SAS) AF: 0.431 AC: 2073 AN: 4812

European-Finnish (FIN) AF: 0.570 AC: 6007 AN: 10544

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41847 AN: 67956

Other (OTH) AF: 0.520 AC: 1099 AN: 2112

Alfa AF: 0.578 Hom.: 43584

Bravo AF: 0.488

Asia WGS AF: 0.425 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.73
PhyloP100		-2.0
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: rs9285151; hg19: chr13-43814236;