Variant rs13359473 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.986-45C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 1,543,294 control chromosomes in the GnomAD database, including 83,165 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6467 hom., cov: 33)

Exomes 𝑓: 0.33 ( 76698 hom. )

Consequence

FLT4
NM_182925.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.831

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 5-180629044-G-A is Benign according to our data. Variant chr5-180629044-G-A is described in ClinVar as [Benign]. Clinvar id is 263072.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FLT4	NM_182925.5 linkuse as main transcript	c.986-45C>T		intron_variant		ENST00000261937.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLT4	ENST00000261937.11 linkuse as main transcript	c.986-45C>T		intron_variant		1	NM_182925.5	P1	P35916-2

Frequencies

GnomAD3 genomes

AF:

0.275

AC:

41883

AN:

152064

Hom.:

6467

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.335

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.302

Gnomad EAS

AF:

0.0640

Gnomad SAS

AF:

0.357

Gnomad FIN

AF:

0.342

Gnomad MID

AF:

0.385

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.285

GnomAD3 exomes

AF:

0.295

AC:

73033

AN:

247560

Hom.:

11818

AF XY:

0.308

AC XY:

41554

AN XY:

134832

show subpopulations

Gnomad AFR exome

AF:

0.161

Gnomad AMR exome

AF:

0.216

Gnomad ASJ exome

AF:

0.300

Gnomad EAS exome

AF:

0.0542

Gnomad SAS exome

AF:

0.377

Gnomad FIN exome

AF:

0.348

Gnomad NFE exome

AF:

0.344

Gnomad OTH exome

AF:

0.323

GnomAD4 exome

AF:

0.327

AC:

454749

AN:

1391112

Hom.:

76698

Cov.:

AF XY:

0.330

AC XY:

229948

AN XY:

695876

show subpopulations

Gnomad4 AFR exome

AF:

0.161

Gnomad4 AMR exome

AF:

0.218

Gnomad4 ASJ exome

AF:

0.301

Gnomad4 EAS exome

AF:

0.0790

Gnomad4 SAS exome

AF:

0.379

Gnomad4 FIN exome

AF:

0.352

Gnomad4 NFE exome

AF:

0.341

Gnomad4 OTH exome

AF:

0.317

GnomAD4 genome

AF:

0.275

AC:

41882

AN:

152182

Hom.:

6467

Cov.:

AF XY:

0.279

AC XY:

20740

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.165

Gnomad4 AMR

AF:

0.262

Gnomad4 ASJ

AF:

0.302

Gnomad4 EAS

AF:

0.0640

Gnomad4 SAS

AF:

0.356

Gnomad4 FIN

AF:

0.342

Gnomad4 NFE

AF:

0.343

Gnomad4 OTH

AF:

0.282

Alfa

AF:

0.245

Hom.:

939

Bravo

AF:

0.258

Asia WGS

AF:

0.203

AC:

709

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

-0.94

CADD

Benign

4.9

DANN

Benign

0.39

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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