rs10085109

Variant names:

• chr5-180633804-G-C
• rs10085109
• NM_182925.5:c.59-2026C>G

Your query was ambiguous. Multiple possible variants found:

• chr5-180633804-G-C
• chr5-180633804-G-T

Variant summary

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

The NM_182925.5(FLT4):​c.59-2026C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,074 control chromosomes in the GnomAD database, including 17,722 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 0.47 (17722 hom., cov: 32)
• Consequence: FLT4 NM_182925.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748

Genes affected

FLT4 (HGNC:3767): (fms related receptor tyrosine kinase 4) This gene encodes a tyrosine kinase receptor for vascular endothelial growth factors C and D. The protein is thought to be involved in lymphangiogenesis and maintenance of the lymphatic endothelium. Mutations in this gene cause hereditary lymphedema type IA. [provided by RefSeq, Jul 2008]

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 (AMR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FLT4	NM_182925.5	c.59-2026C>G		intron_variant	Intron 1 of 29	ENST00000261937.11	NP_891555.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLT4	ENST00000261937.11	c.59-2026C>G		intron_variant	Intron 1 of 29	1	NM_182925.5	ENSP00000261937.6

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72097 AN: 151956 Hom.: 17712 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.474 AC: 72131 AN: 152074 Hom.: 17722 Cov.: 32 AF XY: 0.471 AC XY: 35037 AN XY: 74346

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.501

Alfa AF: 0.355 Hom.: 949

Bravo AF: 0.475

Asia WGS AF: 0.448 AC: 1557 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	0.41
DANN	Benign	0.32

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: rs10085109; hg19: chr5-180060804;