rs13001694

Positions:

• chr2-177254262-A-G

Variant summary

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

The NM_006164.5(NFE2L2):​c.45+10270T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,112 control chromosomes in the GnomAD database, including 8,479 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 0.33 (8479 hom., cov: 32)
• Consequence: NFE2L2 NM_006164.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

NFE2L2 (HGNC:7782): (NFE2 like bZIP transcription factor 2) This gene encodes a transcription factor which is a member of a small family of basic leucine zipper (bZIP) proteins. The encoded transcription factor regulates genes which contain antioxidant response elements (ARE) in their promoters; many of these genes encode proteins involved in response to injury and inflammation which includes the production of free radicals. Multiple transcript variants encoding different isoforms have been characterized for this gene. [provided by RefSeq, Sep 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NFE2L2	NM_006164.5	c.45+10270T>C		intron_variant		ENST00000397062.8	NP_006155.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFE2L2	ENST00000397062.8	c.45+10270T>C		intron_variant		1	NM_006164.5	ENSP00000380252	A1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49846 AN: 151994 Hom.: 8466 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.328 AC: 49886 AN: 152112 Hom.: 8479 Cov.: 32 AF XY: 0.319 AC XY: 23694 AN XY: 74370

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.365

Alfa AF: 0.361 Hom.: 16622

Bravo AF: 0.331

Asia WGS AF: 0.162 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.48
DANN	Benign	0.33

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: rs13001694; hg19: chr2-178118990;