Variant rs59410886 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 ENST00000261937.11(FLT4):c.400+17G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0184 in 1,612,380 control chromosomes in the GnomAD database, including 3,538 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.022 ( 434 hom., cov: 32)

Exomes 𝑓: 0.018 ( 3104 hom. )

Consequence

FLT4
ENST00000261937.11 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.51

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:

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=-0.87).

BP6

Variant 5-180630538-C-T is Benign according to our data. Variant chr5-180630538-C-T is described in ClinVar as [Benign]. Clinvar id is 263058.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-180630538-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 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.400+17G>A		intron_variant		ENST00000261937.11	NP_891555.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLT4	ENST00000261937.11 linkuse as main transcript	c.400+17G>A		intron_variant		1	NM_182925.5	ENSP00000261937	P1	P35916-2

Frequencies

GnomAD3 genomes

AF:

0.0224

AC:

3402

AN:

152044

Hom.:

428

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00162

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0219

Gnomad ASJ

AF:

0.0262

Gnomad EAS

AF:

0.398

Gnomad SAS

AF:

0.0260

Gnomad FIN

AF:

0.0428

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00344

Gnomad OTH

AF:

0.0240

GnomAD3 exomes

AF:

0.0490

AC:

12137

AN:

247934

Hom.:

1782

AF XY:

0.0450

AC XY:

6066

AN XY:

134770

show subpopulations

Gnomad AFR exome

AF:

0.00207

Gnomad AMR exome

AF:

0.0573

Gnomad ASJ exome

AF:

0.0291

Gnomad EAS exome

AF:

0.429

Gnomad SAS exome

AF:

0.0138

Gnomad FIN exome

AF:

0.0416

Gnomad NFE exome

AF:

0.00474

Gnomad OTH exome

AF:

0.0295

GnomAD4 exome

AF:

0.0180

AC:

26319

AN:

1460218

Hom.:

3104

Cov.:

AF XY:

0.0179

AC XY:

12995

AN XY:

726416

show subpopulations

Gnomad4 AFR exome

AF:

0.00218

Gnomad4 AMR exome

AF:

0.0513

Gnomad4 ASJ exome

AF:

0.0281

Gnomad4 EAS exome

AF:

0.377

Gnomad4 SAS exome

AF:

0.0162

Gnomad4 FIN exome

AF:

0.0392

Gnomad4 NFE exome

AF:

0.00268

Gnomad4 OTH exome

AF:

0.0279

GnomAD4 genome

AF:

0.0225

AC:

3421

AN:

152162

Hom.:

434

Cov.:

AF XY:

0.0266

AC XY:

1980

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.00161

Gnomad4 AMR

AF:

0.0222

Gnomad4 ASJ

AF:

0.0262

Gnomad4 EAS

AF:

0.399

Gnomad4 SAS

AF:

0.0263

Gnomad4 FIN

AF:

0.0428

Gnomad4 NFE

AF:

0.00344

Gnomad4 OTH

AF:

0.0304

Alfa

AF:

0.0146

Hom.:

Bravo

AF:

0.0266

Asia WGS

AF:

0.169

AC:

585

AN:

3478

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

-0.87

CADD

Benign

0.38

DANN

Benign

0.69

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