rs615529

Variant names:

• chr13-28472190-T-C
• rs615529
• NM_002019.4:c.65-4573A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002019.4(FLT1):​c.65-4573A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,234 control chromosomes in the GnomAD database, including 1,218 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 0.11 (1218 hom., cov: 32)
• Consequence: FLT1 NM_002019.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309
• Publications: 4 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FLT1	NM_002019.4	c.65-4573A>G		intron_variant	Intron 1 of 29	ENST00000282397.9	NP_002010.2
FLT1	NM_001160030.2	c.65-4573A>G		intron_variant	Intron 1 of 14		NP_001153502.1
FLT1	NM_001159920.2	c.65-4573A>G		intron_variant	Intron 1 of 12		NP_001153392.1
FLT1	NM_001160031.1	c.65-4573A>G		intron_variant	Intron 1 of 11		NP_001153503.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLT1	ENST00000282397.9	c.65-4573A>G		intron_variant	Intron 1 of 29	1	NM_002019.4	ENSP00000282397.4

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17165 AN: 152116 Hom.: 1209 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.0389

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.0915

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.113 AC: 17215 AN: 152234 Hom.: 1218 Cov.: 32 AF XY: 0.114 AC XY: 8464 AN XY: 74442

African (AFR) AF: 0.159 AC: 6586 AN: 41530

American (AMR) AF: 0.199 AC: 3045 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0562 AC: 195 AN: 3472

East Asian (EAS) AF: 0.0392 AC: 203 AN: 5182

South Asian (SAS) AF: 0.0822 AC: 396 AN: 4820

European-Finnish (FIN) AF: 0.0915 AC: 970 AN: 10598

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0820 AC: 5577 AN: 68022

Other (OTH) AF: 0.102 AC: 215 AN: 2112

Alfa AF: 0.0950 Hom.: 425

Bravo AF: 0.123

Asia WGS AF: 0.0670 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.63
PhyloP100		0.31
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs615529; hg19: chr13-29046327;