chr7-26185068-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004289.7(NFE2L3):c.1370C>A(p.Ser457Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,572 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004289.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFE2L3 | NM_004289.7 | c.1370C>A | p.Ser457Tyr | missense_variant | 4/4 | ENST00000056233.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFE2L3 | ENST00000056233.4 | c.1370C>A | p.Ser457Tyr | missense_variant | 4/4 | 1 | NM_004289.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251086Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135700
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461438Hom.: 0 Cov.: 33 AF XY: 0.00000688 AC XY: 5AN XY: 727042
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 07, 2022 | The c.1370C>A (p.S457Y) alteration is located in exon 4 (coding exon 4) of the NFE2L3 gene. This alteration results from a C to A substitution at nucleotide position 1370, causing the serine (S) at amino acid position 457 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at