13-28398027-A-G

Position:

• chr13-28398027-A-G

Variant summary

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

The NM_002019.4(FLT1):​c.1552-959T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,934 control chromosomes in the GnomAD database, including 15,212 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 0.42 (15212 hom., cov: 31)
• Consequence: FLT1 NM_002019.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

FLT1 (HGNC:3763): (fms related receptor tyrosine kinase 1) This gene encodes a member of the vascular endothelial growth factor receptor (VEGFR) family. VEGFR family members are receptor tyrosine kinases (RTKs) which contain an extracellular ligand-binding region with seven immunoglobulin (Ig)-like domains, a transmembrane segment, and a tyrosine kinase (TK) domain within the cytoplasmic domain. This protein binds to VEGFR-A, VEGFR-B and placental growth factor and plays an important role in angiogenesis and vasculogenesis. Expression of this receptor is found in vascular endothelial cells, placental trophoblast cells and peripheral blood monocytes. Multiple transcript variants encoding different isoforms have been found for this gene. Isoforms include a full-length transmembrane receptor isoform and shortened, soluble isoforms. The soluble isoforms are associated with the onset of pre-eclampsia.[provided by RefSeq, May 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FLT1	NM_002019.4	c.1552-959T>C		intron_variant		ENST00000282397.9
FLT1	NM_001159920.2	c.1552-959T>C		intron_variant
FLT1	NM_001160030.2	c.1552-959T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLT1	ENST00000282397.9	c.1552-959T>C		intron_variant		1	NM_002019.4	P1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63690 AN: 151816 Hom.: 15215 Cov.: 31

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.419 AC: 63698 AN: 151934 Hom.: 15212 Cov.: 31 AF XY: 0.419 AC XY: 31105 AN XY: 74212

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.456

Alfa AF: 0.499 Hom.: 9545

Bravo AF: 0.410

Asia WGS AF: 0.499 AC: 1732 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.052
DANN	Benign	0.78

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: rs9319427; hg19: chr13-28972164;