Variant 5-180629863-C-T 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.677-28G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0359 in 1,612,426 control chromosomes in the GnomAD database, including 1,161 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.042 ( 151 hom., cov: 33)

Exomes 𝑓: 0.035 ( 1010 hom. )

Consequence

FLT4
ENST00000261937.11 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.00

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=-0.93).

BP6

Variant 5-180629863-C-T is Benign according to our data. Variant chr5-180629863-C-T is described in ClinVar as [Benign]. Clinvar id is 263070.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-180629863-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0631 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.677-28G>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.677-28G>A		intron_variant		1	NM_182925.5	ENSP00000261937	P1	P35916-2

Frequencies

GnomAD3 genomes

AF:

0.0422

AC:

6416

AN:

152190

Hom.:

150

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0651

Gnomad AMI

AF:

0.0669

Gnomad AMR

AF:

0.0298

Gnomad ASJ

AF:

0.0259

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0199

Gnomad FIN

AF:

0.0397

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0368

Gnomad OTH

AF:

0.0325

GnomAD3 exomes

AF:

0.0313

AC:

7783

AN:

248412

Hom.:

156

AF XY:

0.0313

AC XY:

4215

AN XY:

134862

show subpopulations

Gnomad AFR exome

AF:

0.0675

Gnomad AMR exome

AF:

0.0165

Gnomad ASJ exome

AF:

0.0303

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0213

Gnomad FIN exome

AF:

0.0362

Gnomad NFE exome

AF:

0.0374

Gnomad OTH exome

AF:

0.0378

GnomAD4 exome

AF:

0.0352

AC:

51415

AN:

1460118

Hom.:

1010

Cov.:

AF XY:

0.0348

AC XY:

25256

AN XY:

726284

show subpopulations

Gnomad4 AFR exome

AF:

0.0682

Gnomad4 AMR exome

AF:

0.0183

Gnomad4 ASJ exome

AF:

0.0294

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0208

Gnomad4 FIN exome

AF:

0.0369

Gnomad4 NFE exome

AF:

0.0371

Gnomad4 OTH exome

AF:

0.0375

GnomAD4 genome

AF:

0.0422

AC:

6427

AN:

152308

Hom.:

151

Cov.:

AF XY:

0.0424

AC XY:

3157

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.0651

Gnomad4 AMR

AF:

0.0298

Gnomad4 ASJ

AF:

0.0259

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0199

Gnomad4 FIN

AF:

0.0397

Gnomad4 NFE

AF:

0.0368

Gnomad4 OTH

AF:

0.0317

Alfa

AF:

0.0224

Hom.:

Bravo

AF:

0.0427

Asia WGS

AF:

0.0150

AC:

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 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.032

DANN

Benign

0.71

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