13-28439277-G-C

Position:

• chr13-28439277-G-C

Variant summary

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

The NM_002019.4(FLT1):​c.389-932C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,108 control chromosomes in the GnomAD database, including 46,473 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 0.78 (46473 hom., cov: 31)
• Consequence: FLT1 NM_002019.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLT1	NM_002019.4	c.389-932C>G		intron_variant		ENST00000282397.9	NP_002010.2
FLT1	NM_001159920.2	c.389-932C>G		intron_variant			NP_001153392.1
FLT1	NM_001160030.2	c.389-932C>G		intron_variant			NP_001153502.1
FLT1	NM_001160031.1	c.389-932C>G		intron_variant			NP_001153503.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLT1	ENST00000282397.9	c.389-932C>G		intron_variant		1	NM_002019.4	ENSP00000282397	P1

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118592 AN: 151990 Hom.: 46447 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.780 AC: 118672 AN: 152108 Hom.: 46473 Cov.: 31 AF XY: 0.775 AC XY: 57646 AN XY: 74360

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.752

Alfa AF: 0.791 Hom.: 5552

Bravo AF: 0.781

Asia WGS AF: 0.624 AC: 2168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.76
DANN	Benign	0.30

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: rs4771249; hg19: chr13-29013414;