chr13-28018409-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004119.3(FLT3):c.2541+58A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 1,594,688 control chromosomes in the GnomAD database, including 41,047 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.21 ( 3568 hom., cov: 32)
Exomes 𝑓: 0.22 ( 37479 hom. )
Consequence
FLT3
NM_004119.3 intron
NM_004119.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.465
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 13-28018409-T-C is Benign according to our data. Variant chr13-28018409-T-C is described in ClinVar as [Benign]. Clinvar id is 1245510.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLT3 | NM_004119.3 | c.2541+58A>G | intron_variant | ENST00000241453.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLT3 | ENST00000241453.12 | c.2541+58A>G | intron_variant | 1 | NM_004119.3 | P1 | |||
FLT3 | ENST00000380987.2 | c.*453+58A>G | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.206 AC: 31399AN: 152078Hom.: 3567 Cov.: 32
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GnomAD3 exomes AF: 0.238 AC: 58413AN: 245906Hom.: 7661 AF XY: 0.247 AC XY: 32930AN XY: 133162
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GnomAD4 exome AF: 0.219 AC: 316554AN: 1442492Hom.: 37479 Cov.: 26 AF XY: 0.226 AC XY: 162079AN XY: 716656
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GnomAD4 genome AF: 0.206 AC: 31422AN: 152196Hom.: 3568 Cov.: 32 AF XY: 0.211 AC XY: 15690AN XY: 74410
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 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