13-28015358-C-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004119.3(FLT3):c.2654-102G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 857,866 control chromosomes in the GnomAD database, including 61,629 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.32 ( 8728 hom., cov: 30)
Exomes 𝑓: 0.37 ( 52901 hom. )
Consequence
FLT3
NM_004119.3 intron
NM_004119.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.612
Genes affected
FLT3 (HGNC:3765): (fms related receptor tyrosine kinase 3) This gene encodes a class III receptor tyrosine kinase that regulates hematopoiesis. This receptor is activated by binding of the fms-related tyrosine kinase 3 ligand to the extracellular domain, which induces homodimer formation in the plasma membrane leading to autophosphorylation of the receptor. The activated receptor kinase subsequently phosphorylates and activates multiple cytoplasmic effector molecules in pathways involved in apoptosis, proliferation, and differentiation of hematopoietic cells in bone marrow. Mutations that result in the constitutive activation of this receptor result in acute myeloid leukemia and acute lymphoblastic leukemia. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 13-28015358-C-G is Benign according to our data. Variant chr13-28015358-C-G is described in ClinVar as [Benign]. Clinvar id is 1283726.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FLT3 | NM_004119.3 | c.2654-102G>C | intron_variant | ENST00000241453.12 | NP_004110.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLT3 | ENST00000241453.12 | c.2654-102G>C | intron_variant | 1 | NM_004119.3 | ENSP00000241453 | P1 | |||
FLT3 | ENST00000380987.2 | c.*566-102G>C | intron_variant, NMD_transcript_variant | 1 | ENSP00000370374 |
Frequencies
GnomAD3 genomes AF: 0.316 AC: 47995AN: 151836Hom.: 8725 Cov.: 30
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GnomAD4 exome AF: 0.373 AC: 263296AN: 705910Hom.: 52901 AF XY: 0.369 AC XY: 137894AN XY: 373240
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GnomAD4 genome AF: 0.316 AC: 47989AN: 151956Hom.: 8728 Cov.: 30 AF XY: 0.307 AC XY: 22776AN XY: 74258
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 18, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at