Variant 5-180609871-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_182925.5(FLT4):c.3807+34G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.061 in 1,613,224 control chromosomes in the GnomAD database, including 3,693 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 295 hom., cov: 33)

Exomes 𝑓: 0.062 ( 3398 hom. )

Consequence

FLT4
NM_182925.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.306

Variant links:

Genes affected

FLT4 (HGNC:3767): (fms related receptor tyrosine kinase 4) This gene encodes a tyrosine kinase receptor for vascular endothelial growth factors C and D. The protein is thought to be involved in lymphangiogenesis and maintenance of the lymphatic endothelium. Mutations in this gene cause hereditary lymphedema type IA. [provided by RefSeq, Jul 2008]

FLT4 links:

FLT4 (HGNC:):

FLT4 links:

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=-0.89).

BP6

Variant 5-180609871-C-G is Benign according to our data. Variant chr5-180609871-C-G is described in ClinVar as [Benign]. Clinvar id is 263052.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLT4	NM_182925.5 linkuse as main transcript	c.3807+34G>C		intron_variant		ENST00000261937.11	NP_891555.2	P35916-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLT4	ENST00000261937.11 linkuse as main transcript	c.3807+34G>C		intron_variant		1	NM_182925.5	ENSP00000261937.6		P35916-2

Frequencies

GnomAD3 genomes

AF:

0.0561

AC:

8536

AN:

152136

Hom.:

295

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0465

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0373

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.0279

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0561

Gnomad OTH

AF:

0.0579

GnomAD3 exomes

AF:

0.0682

AC:

17013

AN:

249578

Hom.:

796

AF XY:

0.0729

AC XY:

9843

AN XY:

135024

show subpopulations

Gnomad AFR exome

AF:

0.0442

Gnomad AMR exome

AF:

0.0384

Gnomad ASJ exome

AF:

0.110

Gnomad EAS exome

AF:

0.133

Gnomad SAS exome

AF:

0.136

Gnomad FIN exome

AF:

0.0279

Gnomad NFE exome

AF:

0.0557

Gnomad OTH exome

AF:

0.0687

GnomAD4 exome

AF:

0.0615

AC:

89853

AN:

1460970

Hom.:

3398

Cov.:

AF XY:

0.0640

AC XY:

46528

AN XY:

726794

show subpopulations

Gnomad4 AFR exome

AF:

0.0486

Gnomad4 AMR exome

AF:

0.0401

Gnomad4 ASJ exome

AF:

0.109

Gnomad4 EAS exome

AF:

0.150

Gnomad4 SAS exome

AF:

0.133

Gnomad4 FIN exome

AF:

0.0272

Gnomad4 NFE exome

AF:

0.0542

Gnomad4 OTH exome

AF:

0.0671

GnomAD4 genome

AF:

0.0560

AC:

8533

AN:

152254

Hom.:

295

Cov.:

AF XY:

0.0562

AC XY:

4188

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.0465

Gnomad4 AMR

AF:

0.0372

Gnomad4 ASJ

AF:

0.115

Gnomad4 EAS

AF:

0.138

Gnomad4 SAS

AF:

0.136

Gnomad4 FIN

AF:

0.0279

Gnomad4 NFE

AF:

0.0561

Gnomad4 OTH

AF:

0.0587

Alfa

AF:

0.0356

Hom.:

Bravo

AF:

0.0558

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.2

DANN

Benign

0.42

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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