13-28015358-C-G

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.612
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]

Genome browser will be placed here

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
FLT3NM_004119.3 linkuse as main transcriptc.2654-102G>C intron_variant ENST00000241453.12 NP_004110.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FLT3ENST00000241453.12 linkuse as main transcriptc.2654-102G>C intron_variant 1 NM_004119.3 ENSP00000241453 P1P36888-1
FLT3ENST00000380987.2 linkuse as main transcriptc.*566-102G>C intron_variant, NMD_transcript_variant 1 ENSP00000370374

Frequencies

GnomAD3 genomes
AF:
0.316
AC:
47995
AN:
151836
Hom.:
8725
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.155
Gnomad AMI
AF:
0.405
Gnomad AMR
AF:
0.291
Gnomad ASJ
AF:
0.433
Gnomad EAS
AF:
0.161
Gnomad SAS
AF:
0.227
Gnomad FIN
AF:
0.304
Gnomad MID
AF:
0.405
Gnomad NFE
AF:
0.430
Gnomad OTH
AF:
0.368
GnomAD4 exome
AF:
0.373
AC:
263296
AN:
705910
Hom.:
52901
AF XY:
0.369
AC XY:
137894
AN XY:
373240
show subpopulations
Gnomad4 AFR exome
AF:
0.152
Gnomad4 AMR exome
AF:
0.245
Gnomad4 ASJ exome
AF:
0.440
Gnomad4 EAS exome
AF:
0.154
Gnomad4 SAS exome
AF:
0.243
Gnomad4 FIN exome
AF:
0.317
Gnomad4 NFE exome
AF:
0.429
Gnomad4 OTH exome
AF:
0.369
GnomAD4 genome
AF:
0.316
AC:
47989
AN:
151956
Hom.:
8728
Cov.:
30
AF XY:
0.307
AC XY:
22776
AN XY:
74258
show subpopulations
Gnomad4 AFR
AF:
0.155
Gnomad4 AMR
AF:
0.290
Gnomad4 ASJ
AF:
0.433
Gnomad4 EAS
AF:
0.161
Gnomad4 SAS
AF:
0.228
Gnomad4 FIN
AF:
0.304
Gnomad4 NFE
AF:
0.430
Gnomad4 OTH
AF:
0.365
Alfa
AF:
0.370
Hom.:
1391
Bravo
AF:
0.306
Asia WGS
AF:
0.193
AC:
672
AN:
3478

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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxJun 18, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
5.3
DANN
Benign
0.46

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: rs9579142; hg19: chr13-28589495; COSMIC: COSV54054966; COSMIC: COSV54054966; API