rs144453562
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_182925.5(FLT4):c.1421+19_1421+37del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0279 in 1,598,372 control chromosomes in the GnomAD database, including 2,172 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.060 ( 583 hom., cov: 32)
Exomes 𝑓: 0.024 ( 1589 hom. )
Consequence
FLT4
NM_182925.5 intron
NM_182925.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 5-180625831-TGGCTGTGCAGGGGACCTGA-T is Benign according to our data. Variant chr5-180625831-TGGCTGTGCAGGGGACCTGA-T is described in ClinVar as [Benign]. Clinvar id is 263025.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-180625831-TGGCTGTGCAGGGGACCTGA-T is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLT4 | NM_182925.5 | c.1421+19_1421+37del | intron_variant | ENST00000261937.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLT4 | ENST00000261937.11 | c.1421+19_1421+37del | intron_variant | 1 | NM_182925.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0601 AC: 9134AN: 152052Hom.: 576 Cov.: 32
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GnomAD3 exomes AF: 0.0479 AC: 11413AN: 238210Hom.: 673 AF XY: 0.0432 AC XY: 5624AN XY: 130112
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GnomAD4 exome AF: 0.0244 AC: 35344AN: 1446200Hom.: 1589 AF XY: 0.0241 AC XY: 17338AN XY: 720018
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GnomAD4 genome ? AF: 0.0604 AC: 9185AN: 152172Hom.: 583 Cov.: 32 AF XY: 0.0623 AC XY: 4636AN XY: 74406
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 20, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at