rs200117836
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_182925.5(FLT4):c.2543-14C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000844 in 1,599,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00041 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000050 ( 0 hom. )
Consequence
FLT4
NM_182925.5 splice_polypyrimidine_tract, intron
NM_182925.5 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.87
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 5-180619783-G-A is Benign according to our data. Variant chr5-180619783-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 263038.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-180619783-G-A is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000407 (62/152388) while in subpopulation AFR AF= 0.00147 (61/41596). AF 95% confidence interval is 0.00117. There are 0 homozygotes in gnomad4. There are 26 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLT4 | NM_182925.5 | c.2543-14C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000261937.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLT4 | ENST00000261937.11 | c.2543-14C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_182925.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000414 AC: 63AN: 152270Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000145 AC: 35AN: 242078Hom.: 0 AF XY: 0.0000832 AC XY: 11AN XY: 132136
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GnomAD4 exome AF: 0.0000504 AC: 73AN: 1447564Hom.: 0 Cov.: 30 AF XY: 0.0000555 AC XY: 40AN XY: 720804
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GnomAD4 genome ? AF: 0.000407 AC: 62AN: 152388Hom.: 0 Cov.: 34 AF XY: 0.000349 AC XY: 26AN XY: 74522
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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