chr2-177271901-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000464747.5(NFE2L2):​c.-3-37630T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,180 control chromosomes in the GnomAD database, including 3,851 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 0.22 ( 3851 hom., cov: 32)

Consequence

NFE2L2
ENST00000464747.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.751
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.177271901A>C intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NFE2L2ENST00000699346.1 linkuse as main transcriptc.183+24646T>G intron_variant ENSP00000514321.1 A0A8V8TNM0
NFE2L2ENST00000586532.6 linkuse as main transcriptc.43-37630T>G intron_variant 5 ENSP00000464920.2 K7EIW5
NFE2L2ENST00000699265.1 linkuse as main transcriptc.43-37630T>G intron_variant ENSP00000514246.1 K7EIW5

Frequencies

GnomAD3 genomes
AF:
0.218
AC:
33137
AN:
152062
Hom.:
3848
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.262
Gnomad AMI
AF:
0.497
Gnomad AMR
AF:
0.159
Gnomad ASJ
AF:
0.254
Gnomad EAS
AF:
0.0837
Gnomad SAS
AF:
0.198
Gnomad FIN
AF:
0.220
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.210
Gnomad OTH
AF:
0.202
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.218
AC:
33146
AN:
152180
Hom.:
3851
Cov.:
32
AF XY:
0.215
AC XY:
16010
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.262
Gnomad4 AMR
AF:
0.158
Gnomad4 ASJ
AF:
0.254
Gnomad4 EAS
AF:
0.0833
Gnomad4 SAS
AF:
0.198
Gnomad4 FIN
AF:
0.220
Gnomad4 NFE
AF:
0.210
Gnomad4 OTH
AF:
0.199
Alfa
AF:
0.217
Hom.:
1138
Bravo
AF:
0.218
Asia WGS
AF:
0.118
AC:
410
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
4.4
DANN
Benign
0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs16865105; hg19: chr2-178136629; API