5-180628188-A-G

Position:

• chr5-180628188-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182925.5(FLT4):​c.1103+694T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,154 control chromosomes in the GnomAD database, including 11,329 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.35 (11329 hom., cov: 33)
• Consequence: FLT4 NM_182925.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLT4	NM_182925.5	c.1103+694T>C		intron_variant		ENST00000261937.11	NP_891555.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLT4	ENST00000261937.11	c.1103+694T>C		intron_variant		1	NM_182925.5	ENSP00000261937.6

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53209 AN: 152036 Hom.: 11327 Cov.: 33

Gnomad AFR AF: 0.0931

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.361

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.350 AC: 53204 AN: 152154 Hom.: 11329 Cov.: 33 AF XY: 0.355 AC XY: 26371 AN XY: 74380

Gnomad4 AFR AF: 0.0928

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.359

Alfa AF: 0.418 Hom.: 13129

Bravo AF: 0.333

Asia WGS AF: 0.364 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.72

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

Other links and lift over

dbSNP: rs3797102; hg19: chr5-180055188; COSMIC: COSV56104318; COSMIC: COSV56104318;