chr13-28300516-TACACCCACACACACACACACACACACACACACACACACACAT-CACACACACACACACACACACACACACACACACACACACACACACAC

Variant names:

• chr13-28300516-TACACCCACACACACACACACACACACACACACACACACACAT-CACACACACACACACACACACACACACACACACACACACACACACAC
• rs3138582
• NM_002019.4:c.*2609_*2651delATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGGTGTAinsGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_002019.4(FLT1):​c.*2609_*2651delATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGGTGTAinsGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: FLT1 NM_002019.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.726
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002019.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FLT1	NM_002019.4	MANE Select	c.*2609_*2651delATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGGTGTAinsGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG		3_prime_UTR	Exon 30 of 30	NP_002010.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FLT1	ENST00000282397.9	TSL:1 MANE Select	c.*2609_*2651delATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGGTGTAinsGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG		3_prime_UTR	Exon 30 of 30	ENSP00000282397.4
	FLT1	ENST00000909998.1		c.*2609_*2651delATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGGTGTAinsGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG		3_prime_UTR	Exon 30 of 30	ENSP00000580057.1
	FLT1	ENST00000909997.1		c.*2609_*2651delATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGGTGTAinsGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG		3_prime_UTR	Exon 28 of 28	ENSP00000580056.1

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3138582; hg19: chr13-28874653;