Variant chr5-180616330-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.3219+37G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0472 in 1,613,180 control chromosomes in the GnomAD database, including 2,152 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.037 ( 161 hom., cov: 31)

Exomes 𝑓: 0.048 ( 1991 hom. )

Consequence

FLT4
NM_182925.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.69

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=-1.01).

BP6

Variant 5-180616330-C-G is Benign according to our data. Variant chr5-180616330-C-G is described in ClinVar as [Benign]. Clinvar id is 263045.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0804 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.3219+37G>C		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.3219+37G>C		intron_variant		1	NM_182925.5	ENSP00000261937	P1	P35916-2

Frequencies

GnomAD3 genomes

AF:

0.0366

AC:

5578

AN:

152230

Hom.:

161

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00965

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0326

Gnomad ASJ

AF:

0.0861

Gnomad EAS

AF:

0.0869

Gnomad SAS

AF:

0.0267

Gnomad FIN

AF:

0.0393

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0484

Gnomad OTH

AF:

0.0353

GnomAD3 exomes

AF:

0.0428

AC:

10736

AN:

250730

Hom.:

331

AF XY:

0.0431

AC XY:

5850

AN XY:

135672

show subpopulations

Gnomad AFR exome

AF:

0.00968

Gnomad AMR exome

AF:

0.0237

Gnomad ASJ exome

AF:

0.0880

Gnomad EAS exome

AF:

0.0880

Gnomad SAS exome

AF:

0.0290

Gnomad FIN exome

AF:

0.0368

Gnomad NFE exome

AF:

0.0469

Gnomad OTH exome

AF:

0.0442

GnomAD4 exome

AF:

0.0483

AC:

70518

AN:

1460832

Hom.:

1991

Cov.:

AF XY:

0.0478

AC XY:

34774

AN XY:

726790

show subpopulations

Gnomad4 AFR exome

AF:

0.00768

Gnomad4 AMR exome

AF:

0.0250

Gnomad4 ASJ exome

AF:

0.0822

Gnomad4 EAS exome

AF:

0.103

Gnomad4 SAS exome

AF:

0.0283

Gnomad4 FIN exome

AF:

0.0378

Gnomad4 NFE exome

AF:

0.0498

Gnomad4 OTH exome

AF:

0.0480

GnomAD4 genome

AF:

0.0366

AC:

5580

AN:

152348

Hom.:

161

Cov.:

AF XY:

0.0351

AC XY:

2612

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.00959

Gnomad4 AMR

AF:

0.0325

Gnomad4 ASJ

AF:

0.0861

Gnomad4 EAS

AF:

0.0871

Gnomad4 SAS

AF:

0.0269

Gnomad4 FIN

AF:

0.0393

Gnomad4 NFE

AF:

0.0484

Gnomad4 OTH

AF:

0.0373

Alfa

AF:

0.0303

Hom.:

Bravo

AF:

0.0357

Asia WGS

AF:

0.0530

AC:

187

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

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.0050

DANN

Benign

0.33

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