13-43642928-T-C

Position:

• chr13-43642928-T-C

Variant summary

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

The NM_001347969.2(ENOX1):​c.-219+24551A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,984 control chromosomes in the GnomAD database, including 21,181 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 0.53 (21181 hom., cov: 32)
• Consequence: ENOX1 NM_001347969.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.798

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]

ENOX1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENOX1	NM_001347969.2	c.-219+24551A>G		intron_variant		ENST00000690772.1	NP_001334898.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENOX1	ENST00000690772.1	c.-219+24551A>G		intron_variant			NM_001347969.2	ENSP00000509229.1
ENOX1	ENST00000261488.10	c.-219+24514A>G		intron_variant		1		ENSP00000261488.6

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79841 AN: 151866 Hom.: 21153 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.526 AC: 79909 AN: 151984 Hom.: 21181 Cov.: 32 AF XY: 0.527 AC XY: 39112 AN XY: 74278

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.523

Alfa AF: 0.541 Hom.: 21013

Bravo AF: 0.513

Asia WGS AF: 0.560 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.7
DANN	Benign	0.78

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: rs4942242; hg19: chr13-44217064; COSMIC: COSV54916080;