12-54292400-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001136023.3(NFE2):​c.1096G>A​(p.Gly366Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

NFE2
NM_001136023.3 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.85
Variant links:
Genes affected
NFE2 (HGNC:7780): (nuclear factor, erythroid 2) Enables several functions, including WW domain binding activity; identical protein binding activity; and protein N-terminus binding activity. Contributes to cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including labyrinthine layer blood vessel development; negative regulation of bone mineralization; and negative regulation of syncytium formation by plasma membrane fusion. Part of protein-DNA complex. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3164429).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NFE2NM_001136023.3 linkuse as main transcriptc.1096G>A p.Gly366Arg missense_variant 3/3 ENST00000435572.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NFE2ENST00000435572.7 linkuse as main transcriptc.1096G>A p.Gly366Arg missense_variant 3/31 NM_001136023.3 P1
ENST00000553061.1 linkuse as main transcriptn.545+15225C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMay 18, 2022The c.1096G>A (p.G366R) alteration is located in exon 3 (coding exon 2) of the NFE2 gene. This alteration results from a G to A substitution at nucleotide position 1096, causing the glycine (G) at amino acid position 366 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.19
BayesDel_addAF
Benign
-0.041
T
BayesDel_noAF
Benign
-0.30
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.35
T;T;T;T
Eigen
Benign
-0.020
Eigen_PC
Benign
0.082
FATHMM_MKL
Benign
0.41
N
LIST_S2
Benign
0.78
.;.;.;T
M_CAP
Benign
0.0020
T
MetaRNN
Benign
0.32
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.13
N;N;N;N
MutationTaster
Benign
0.65
N;N;N;N
PrimateAI
Uncertain
0.56
T
PROVEAN
Benign
-0.96
N;N;N;N
REVEL
Benign
0.086
Sift
Benign
0.081
T;T;T;T
Sift4G
Benign
0.15
T;T;T;T
Polyphen
0.62
P;P;P;P
Vest4
0.43
MutPred
0.28
Gain of catalytic residue at F361 (P = 0.0207);Gain of catalytic residue at F361 (P = 0.0207);Gain of catalytic residue at F361 (P = 0.0207);Gain of catalytic residue at F361 (P = 0.0207);
MVP
0.20
MPC
0.98
ClinPred
0.77
D
GERP RS
5.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.084
gMVP
0.11

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

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

Other links and lift over

dbSNP: rs1944324674; hg19: chr12-54686184; COSMIC: COSV100380848; COSMIC: COSV100380848; API