rs201306288
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_182925.5(FLT4):c.1421+37C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00225 in 1,514,824 control chromosomes in the GnomAD database, including 71 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.013 ( 34 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 37 hom. )
Consequence
FLT4
NM_182925.5 intron
NM_182925.5 intron
Scores
2
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 5-180625832-G-A is Benign according to our data. Variant chr5-180625832-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 263026.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0512 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLT4 | NM_182925.5 | c.1421+37C>T | intron_variant | ENST00000261937.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLT4 | ENST00000261937.11 | c.1421+37C>T | intron_variant | 1 | NM_182925.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0131 AC: 1770AN: 135474Hom.: 34 Cov.: 32
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GnomAD3 exomes AF: 0.00275 AC: 655AN: 238536Hom.: 12 AF XY: 0.00207 AC XY: 269AN XY: 130256
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GnomAD4 exome AF: 0.00118 AC: 1633AN: 1379316Hom.: 37 Cov.: 29 AF XY: 0.00100 AC XY: 690AN XY: 687096
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GnomAD4 genome ? AF: 0.0131 AC: 1775AN: 135508Hom.: 34 Cov.: 32 AF XY: 0.0126 AC XY: 832AN XY: 65994
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at