rs138954560
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_182925.5(FLT4):c.59-24C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00188 in 1,538,962 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.010 ( 20 hom., cov: 33)
Exomes 𝑓: 0.00099 ( 18 hom. )
Consequence
FLT4
NM_182925.5 intron
NM_182925.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.32
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=-0.9).
BP6
?
Variant 5-180631802-G-A is Benign according to our data. Variant chr5-180631802-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 263066.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00996 (1517/152298) while in subpopulation AFR AF= 0.0345 (1432/41560). AF 95% confidence interval is 0.033. There are 20 homozygotes in gnomad4. There are 731 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 20 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLT4 | NM_182925.5 | c.59-24C>T | intron_variant | ENST00000261937.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLT4 | ENST00000261937.11 | c.59-24C>T | intron_variant | 1 | NM_182925.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00990 AC: 1506AN: 152180Hom.: 19 Cov.: 33
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GnomAD3 exomes AF: 0.00255 AC: 620AN: 243382Hom.: 6 AF XY: 0.00176 AC XY: 233AN XY: 132578
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GnomAD4 exome AF: 0.000991 AC: 1374AN: 1386664Hom.: 18 Cov.: 24 AF XY: 0.000873 AC XY: 606AN XY: 694194
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GnomAD4 genome ? AF: 0.00996 AC: 1517AN: 152298Hom.: 20 Cov.: 33 AF XY: 0.00982 AC XY: 731AN XY: 74472
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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