13-28342206-T-C

Position:

• chr13-28342206-T-C

Variant summary

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

The NM_002019.4(FLT1):​c.2356-2906A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,014 control chromosomes in the GnomAD database, including 25,939 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 0.55 (25939 hom., cov: 31)
• Consequence: FLT1 NM_002019.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLT1	NM_002019.4	c.2356-2906A>G		intron_variant		ENST00000282397.9	NP_002010.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLT1	ENST00000282397.9	c.2356-2906A>G		intron_variant		1	NM_002019.4	ENSP00000282397	P1
FLT1	ENST00000540678.2	n.243-2906A>G		intron_variant, non_coding_transcript_variant		1
FLT1	ENST00000706527.1	n.181-2906A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84140 AN: 151896 Hom.: 25938 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.554 AC: 84156 AN: 152014 Hom.: 25939 Cov.: 31 AF XY: 0.556 AC XY: 41342 AN XY: 74316

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.596

Alfa AF: 0.660 Hom.: 68915

Bravo AF: 0.535

Asia WGS AF: 0.711 AC: 2469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.50

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: rs2387632; hg19: chr13-28916343;