rs141363120
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_006164.5(NFE2L2):c.925C>T(p.Leu309Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00337 in 1,614,194 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L309V) has been classified as Uncertain significance.
Frequency
Consequence
NM_006164.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFE2L2 | NM_006164.5 | c.925C>T | p.Leu309Phe | missense_variant | 5/5 | ENST00000397062.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFE2L2 | ENST00000397062.8 | c.925C>T | p.Leu309Phe | missense_variant | 5/5 | 1 | NM_006164.5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00256 AC: 389AN: 152202Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00301 AC: 751AN: 249802Hom.: 3 AF XY: 0.00289 AC XY: 391AN XY: 135512
GnomAD4 exome AF: 0.00346 AC: 5051AN: 1461874Hom.: 11 Cov.: 31 AF XY: 0.00331 AC XY: 2406AN XY: 727240
GnomAD4 genome ? AF: 0.00255 AC: 389AN: 152320Hom.: 3 Cov.: 33 AF XY: 0.00227 AC XY: 169AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | NFE2L2: BP4, BS1, BS2 - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at