19-10491584-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_203500.2(KEAP1):c.1318G>A(p.Val440Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000816 in 1,543,876 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V440A) has been classified as Uncertain significance.
Frequency
Consequence
NM_203500.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KEAP1 | NM_203500.2 | c.1318G>A | p.Val440Met | missense_variant | 3/6 | ENST00000171111.10 | |
KEAP1 | NM_012289.4 | c.1318G>A | p.Val440Met | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KEAP1 | ENST00000171111.10 | c.1318G>A | p.Val440Met | missense_variant | 3/6 | 1 | NM_203500.2 | P1 | |
KEAP1 | ENST00000393623.6 | c.1318G>A | p.Val440Met | missense_variant | 3/6 | 1 | P1 | ||
KEAP1 | ENST00000592478.5 | c.139G>A | p.Val47Met | missense_variant | 1/3 | 1 | |||
KEAP1 | ENST00000590593.1 | c.298G>A | p.Val100Met | missense_variant, NMD_transcript_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000843 AC: 16AN: 189734Hom.: 0 AF XY: 0.0000880 AC XY: 9AN XY: 102220
GnomAD4 exome AF: 0.0000826 AC: 115AN: 1391528Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 74AN XY: 685234
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74510
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.1318G>A (p.V440M) alteration is located in exon 3 (coding exon 2) of the KEAP1 gene. This alteration results from a G to A substitution at nucleotide position 1318, causing the valine (V) at amino acid position 440 to be replaced by a methionine (M). 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