rs12858139

chr13-28483931-A-C

Variant summary

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

The NM_002019.4(FLT1):c.64+10849T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 152,018 control chromosomes in the GnomAD database, including 17,386 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 0.45 (17386 hom., cov: 32)
• Consequence: FLT1 NM_002019.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FLT1	NM_002019.4	c.64+10849T>G		intron_variant		ENST00000282397.9
FLT1	NM_001159920.2	c.64+10849T>G		intron_variant
FLT1	NM_001160030.2	c.64+10849T>G		intron_variant
FLT1	NM_001160031.1	c.64+10849T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLT1	ENST00000282397.9	c.64+10849T>G		intron_variant		1	NM_002019.4	P1

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68133 AN: 151902 Hom.: 17389 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.448 AC: 68132 AN: 152018 Hom.: 17386 Cov.: 32 AF XY: 0.448 AC XY: 33317 AN XY: 74310

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.513

Alfa AF: 0.484 Hom.: 2373

Bravo AF: 0.442

Asia WGS AF: 0.587 AC: 2043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.3
Dann	Benign	0.58

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: rs12858139; hg19: chr13-29058068;