chr13-43327335-T-C

Variant names:

• chr13-43327335-T-C
• rs4941455
• NM_001347969.2:c.1037-810A>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.1037-810A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,148 control chromosomes in the GnomAD database, including 51,769 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 0.82 (51769 hom., cov: 32)
• Consequence: ENOX1 NM_001347969.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.89 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.1037-810A>G		intron	N/A	NP_001334898.1	A0A024RDT8
	ENOX1	NM_001347963.2		c.1142-810A>G		intron	N/A	NP_001334892.1
	ENOX1	NM_001127615.3		c.1037-810A>G		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.1037-810A>G		intron	N/A	ENSP00000509229.1	Q8TC92-1
	ENOX1	ENST00000261488.10	TSL:1	c.1037-810A>G		intron	N/A	ENSP00000261488.6	Q8TC92-1
	ENOX1	ENST00000871211.1		c.1037-810A>G		intron	N/A	ENSP00000541270.1

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125340 AN: 152030 Hom.: 51713 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.825 AC: 125453 AN: 152148 Hom.: 51769 Cov.: 32 AF XY: 0.825 AC XY: 61361 AN XY: 74386

African (AFR) AF: 0.799 AC: 33165 AN: 41510

American (AMR) AF: 0.790 AC: 12068 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.873 AC: 3031 AN: 3472

East Asian (EAS) AF: 0.820 AC: 4227 AN: 5154

South Asian (SAS) AF: 0.913 AC: 4406 AN: 4828

European-Finnish (FIN) AF: 0.833 AC: 8814 AN: 10584

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57059 AN: 68004

Other (OTH) AF: 0.830 AC: 1754 AN: 2112

Alfa AF: 0.832 Hom.: 139645

Bravo AF: 0.816

Asia WGS AF: 0.885 AC: 3078 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.60
PhyloP100		-0.046
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: rs4941455; hg19: chr13-43901471;