Variant rs7993418 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002019.4(FLT1):c.3639C>T(p.Tyr1213Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 1,585,192 control chromosomes in the GnomAD database, including 500,586 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.69 ( 39117 hom., cov: 32)

Exomes 𝑓: 0.80 ( 461469 hom. )

Consequence

FLT1
NM_002019.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.51

Variant links:

Genes affected

FLT1 (HGNC:3763): (fms related receptor tyrosine kinase 1) This gene encodes a member of the vascular endothelial growth factor receptor (VEGFR) family. VEGFR family members are receptor tyrosine kinases (RTKs) which contain an extracellular ligand-binding region with seven immunoglobulin (Ig)-like domains, a transmembrane segment, and a tyrosine kinase (TK) domain within the cytoplasmic domain. This protein binds to VEGFR-A, VEGFR-B and placental growth factor and plays an important role in angiogenesis and vasculogenesis. Expression of this receptor is found in vascular endothelial cells, placental trophoblast cells and peripheral blood monocytes. Multiple transcript variants encoding different isoforms have been found for this gene. Isoforms include a full-length transmembrane receptor isoform and shortened, soluble isoforms. The soluble isoforms are associated with the onset of pre-eclampsia.[provided by RefSeq, May 2009]

FLT1 links:

FLT1 (HGNC:):

FLT1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP7

Synonymous conserved (PhyloP=-1.51 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLT1	NM_002019.4 linkuse as main transcript	c.3639C>T	p.Tyr1213Tyr	synonymous_variant	28/30	ENST00000282397.9	NP_002010.2	P17948-1L7RSL3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLT1	ENST00000282397.9 linkuse as main transcript	c.3639C>T	p.Tyr1213Tyr	synonymous_variant	28/30	1	NM_002019.4	ENSP00000282397.4		P17948-1

Frequencies

GnomAD3 genomes

AF:

0.686

AC:

104284

AN:

151964

Hom.:

39100

Cov.:

show subpopulations

Gnomad AFR

AF:

0.356

Gnomad AMI

AF:

0.726

Gnomad AMR

AF:

0.815

Gnomad ASJ

AF:

0.854

Gnomad EAS

AF:

0.997

Gnomad SAS

AF:

0.895

Gnomad FIN

AF:

0.795

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.792

Gnomad OTH

AF:

0.731

GnomAD3 exomes

AF:

0.804

AC:

202061

AN:

251330

Hom.:

83632

AF XY:

0.812

AC XY:

110375

AN XY:

135854

show subpopulations

Gnomad AFR exome

AF:

0.345

Gnomad AMR exome

AF:

0.874

Gnomad ASJ exome

AF:

0.850

Gnomad EAS exome

AF:

0.999

Gnomad SAS exome

AF:

0.887

Gnomad FIN exome

AF:

0.784

Gnomad NFE exome

AF:

0.794

Gnomad OTH exome

AF:

0.793

GnomAD4 exome

AF:

0.798

AC:

1143133

AN:

1433110

Hom.:

461469

Cov.:

AF XY:

0.801

AC XY:

573000

AN XY:

715002

show subpopulations

Gnomad4 AFR exome

AF:

0.337

Gnomad4 AMR exome

AF:

0.867

Gnomad4 ASJ exome

AF:

0.849

Gnomad4 EAS exome

AF:

0.999

Gnomad4 SAS exome

AF:

0.882

Gnomad4 FIN exome

AF:

0.786

Gnomad4 NFE exome

AF:

0.795

Gnomad4 OTH exome

AF:

0.786

GnomAD4 genome

AF:

0.686

AC:

104336

AN:

152082

Hom.:

39117

Cov.:

AF XY:

0.696

AC XY:

51752

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.356

Gnomad4 AMR

AF:

0.816

Gnomad4 ASJ

AF:

0.854

Gnomad4 EAS

AF:

0.997

Gnomad4 SAS

AF:

0.896

Gnomad4 FIN

AF:

0.795

Gnomad4 NFE

AF:

0.792

Gnomad4 OTH

AF:

0.733

Alfa

AF:

0.747

Hom.:

22649

Bravo

AF:

0.671

Asia WGS

AF:

0.917

AC:

3189

AN:

3478

EpiCase

AF:

0.793

EpiControl

AF:

0.791

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.10

DANN

Benign

0.45

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over