Variant 13-28319505-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002019.4(FLT1):c.3204T>C(p.Pro1068=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 1,612,098 control chromosomes in the GnomAD database, including 36,238 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.21 ( 3704 hom., cov: 32)

Exomes 𝑓: 0.20 ( 32534 hom. )

Consequence

FLT1
NM_002019.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2O:1

Conservation

PhyloP100: -2.74

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 13-28319505-A-G is Benign according to our data. Variant chr13-28319505-A-G is described in ClinVar as [Benign]. Clinvar id is 162072.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.74 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 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.3204T>C	p.Pro1068=	synonymous_variant	24/30	ENST00000282397.9	NP_002010.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLT1	ENST00000282397.9 linkuse as main transcript	c.3204T>C	p.Pro1068=	synonymous_variant	24/30	1	NM_002019.4	ENSP00000282397	P1	P17948-1

Frequencies

GnomAD3 genomes

AF:

0.210

AC:

32002

AN:

152058

Hom.:

3702

Cov.:

show subpopulations

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.308

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.177

Gnomad SAS

AF:

0.405

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.188

Gnomad OTH

AF:

0.208

GnomAD3 exomes

AF:

0.206

AC:

51709

AN:

250682

Hom.:

6408

AF XY:

0.218

AC XY:

29550

AN XY:

135472

show subpopulations

Gnomad AFR exome

AF:

0.272

Gnomad AMR exome

AF:

0.0958

Gnomad ASJ exome

AF:

0.240

Gnomad EAS exome

AF:

0.184

Gnomad SAS exome

AF:

0.411

Gnomad FIN exome

AF:

0.125

Gnomad NFE exome

AF:

0.191

Gnomad OTH exome

AF:

0.206

GnomAD4 exome

AF:

0.201

AC:

293329

AN:

1459922

Hom.:

32534

Cov.:

AF XY:

0.208

AC XY:

150840

AN XY:

726356

show subpopulations

Gnomad4 AFR exome

AF:

0.272

Gnomad4 AMR exome

AF:

0.101

Gnomad4 ASJ exome

AF:

0.243

Gnomad4 EAS exome

AF:

0.161

Gnomad4 SAS exome

AF:

0.407

Gnomad4 FIN exome

AF:

0.134

Gnomad4 NFE exome

AF:

0.189

Gnomad4 OTH exome

AF:

0.220

GnomAD4 genome

AF:

0.210

AC:

32017

AN:

152176

Hom.:

3704

Cov.:

AF XY:

0.209

AC XY:

15524

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.275

Gnomad4 AMR

AF:

0.125

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.177

Gnomad4 SAS

AF:

0.406

Gnomad4 FIN

AF:

0.123

Gnomad4 NFE

AF:

0.188

Gnomad4 OTH

AF:

0.209

Alfa

AF:

0.194

Hom.:

5246

Bravo

AF:

0.208

Asia WGS

AF:

0.269

AC:

936

AN:

3478

EpiCase

AF:

0.198

EpiControl

AF:

0.202

ClinVar

Significance: Benign

Submissions summary: Benign:2Other:1

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	Jul 13, 2018	- -

Carcinoma of colon

Other:1

not provided, no classification provided

not provided

Immunobiology Lab; University of Kashmir

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

0.82

DANN

Benign

0.64

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over