chr13-28018483-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 9P and 4B. PM1PM5PP3_StrongPP5BS2
The NM_004119.3(FLT3):c.2525A>G(p.Tyr842Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,614,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y842H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_004119.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLT3 | NM_004119.3 | c.2525A>G | p.Tyr842Cys | missense_variant | 20/24 | ENST00000241453.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLT3 | ENST00000241453.12 | c.2525A>G | p.Tyr842Cys | missense_variant | 20/24 | 1 | NM_004119.3 | P1 | |
FLT3 | ENST00000380987.2 | c.*437A>G | 3_prime_UTR_variant, NMD_transcript_variant | 21/25 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249106Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134850
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461764Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727188
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74452
ClinVar
Submissions by phenotype
Acute myeloid leukemia Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Database of Curated Mutations (DoCM) | Dec 26, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at