rs1933437
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004119.3(FLT3):c.680C>T(p.Thr227Met) variant causes a missense change. The variant allele was found at a frequency of 0.608 in 1,613,410 control chromosomes in the GnomAD database, including 302,489 homozygotes. 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004119.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLT3 | NM_004119.3 | c.680C>T | p.Thr227Met | missense_variant | 6/24 | ENST00000241453.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLT3 | ENST00000241453.12 | c.680C>T | p.Thr227Met | missense_variant | 6/24 | 1 | NM_004119.3 | P1 | |
FLT3 | ENST00000380987.2 | c.680C>T | p.Thr227Met | missense_variant, NMD_transcript_variant | 6/25 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.532 AC: 80895AN: 151936Hom.: 22648 Cov.: 33
GnomAD3 exomes AF: 0.605 AC: 152050AN: 251366Hom.: 46973 AF XY: 0.609 AC XY: 82690AN XY: 135852
GnomAD4 exome AF: 0.616 AC: 900045AN: 1461354Hom.: 279825 Cov.: 40 AF XY: 0.616 AC XY: 447763AN XY: 727010
GnomAD4 genome ? AF: 0.532 AC: 80931AN: 152056Hom.: 22664 Cov.: 33 AF XY: 0.534 AC XY: 39731AN XY: 74334
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
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