chr13-43260134-C-T

Variant names:

• chr13-43260134-C-T
• rs17538444
• NM_001347969.2:c.1611+5264G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.064 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENOX1	NM_001347969.2	MANE Select	c.1611+5264G>A		intron	N/A	NP_001334898.1	A0A024RDT8
	ENOX1	NM_001347963.2		c.1716+5264G>A		intron	N/A	NP_001334892.1
	ENOX1	NM_001127615.3		c.1611+5264G>A		intron	N/A	NP_001121087.1	A0A024RDT8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENOX1	ENST00000690772.1	MANE Select	c.1611+5264G>A		intron	N/A	ENSP00000509229.1	Q8TC92-1
	ENOX1	ENST00000261488.10	TSL:1	c.1611+5264G>A		intron	N/A	ENSP00000261488.6	Q8TC92-1
	ENOX1	ENST00000871211.1		c.1611+5264G>A		intron	N/A	ENSP00000541270.1

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

African (AFR) AF: 0.0381 AC: 1582 AN: 41550

American (AMR) AF: 0.0351 AC: 537 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3472

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5190

South Asian (SAS) AF: 0.0501 AC: 242 AN: 4830

European-Finnish (FIN) AF: 0.0523 AC: 555 AN: 10614

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0656 AC: 4464 AN: 68020

Other (OTH) AF: 0.0525 AC: 111 AN: 2116

Alfa AF: 0.0563 Hom.: 290

Bravo AF: 0.0482

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.7
DANN	Benign	0.74
PhyloP100		0.15
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: rs17538444; hg19: chr13-43834270;