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13-28015372-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_004119.3(FLT3):c.2654-116G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 794,854 control chromosomes in the GnomAD database, including 50,939 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.30 ( 7988 hom., cov: 30)
Exomes 𝑓: 0.35 ( 42951 hom. )

Consequence

FLT3
NM_004119.3 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.00
Variant links:
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=-0.94).
BP6
Variant 13-28015372-C-T is Benign according to our data. Variant chr13-28015372-C-T is described in ClinVar as [Benign]. Clinvar id is 1277163.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FLT3NM_004119.3 linkuse as main transcriptc.2654-116G>A intron_variant ENST00000241453.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FLT3ENST00000241453.12 linkuse as main transcriptc.2654-116G>A intron_variant 1 NM_004119.3 P1P36888-1
FLT3ENST00000380987.2 linkuse as main transcriptc.*566-116G>A intron_variant, NMD_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.303
AC:
46027
AN:
151682
Hom.:
7984
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.152
Gnomad AMI
AF:
0.400
Gnomad AMR
AF:
0.282
Gnomad ASJ
AF:
0.415
Gnomad EAS
AF:
0.151
Gnomad SAS
AF:
0.215
Gnomad FIN
AF:
0.289
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.412
Gnomad OTH
AF:
0.350
GnomAD4 exome
AF:
0.352
AC:
226371
AN:
643052
Hom.:
42951
AF XY:
0.348
AC XY:
119393
AN XY:
342790
show subpopulations
Gnomad4 AFR exome
AF:
0.151
Gnomad4 AMR exome
AF:
0.245
Gnomad4 ASJ exome
AF:
0.419
Gnomad4 EAS exome
AF:
0.152
Gnomad4 SAS exome
AF:
0.231
Gnomad4 FIN exome
AF:
0.301
Gnomad4 NFE exome
AF:
0.406
Gnomad4 OTH exome
AF:
0.352
GnomAD4 genome
AF:
0.303
AC:
46028
AN:
151802
Hom.:
7988
Cov.:
30
AF XY:
0.295
AC XY:
21866
AN XY:
74186
show subpopulations
Gnomad4 AFR
AF:
0.152
Gnomad4 AMR
AF:
0.282
Gnomad4 ASJ
AF:
0.415
Gnomad4 EAS
AF:
0.151
Gnomad4 SAS
AF:
0.216
Gnomad4 FIN
AF:
0.289
Gnomad4 NFE
AF:
0.412
Gnomad4 OTH
AF:
0.348
Alfa
AF:
0.388
Hom.:
11380
Bravo
AF:
0.295
Asia WGS
AF:
0.187
AC:
652
AN:
3478

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 submitterclinical testingGeneDxJun 18, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
Cadd
Benign
0.63
Dann
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9579143; hg19: chr13-28589509; API