rs34117331
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_182925.5(FLT4):āc.633A>Gā(p.Gly211=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00571 in 1,612,830 control chromosomes in the GnomAD database, including 295 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.023 ( 135 hom., cov: 33)
Exomes š: 0.0039 ( 160 hom. )
Consequence
FLT4
NM_182925.5 synonymous
NM_182925.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.66
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 5-180629986-T-C is Benign according to our data. Variant chr5-180629986-T-C is described in ClinVar as [Benign]. Clinvar id is 263067.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-180629986-T-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-1.65 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0716 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLT4 | NM_182925.5 | c.633A>G | p.Gly211= | synonymous_variant | 5/30 | ENST00000261937.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLT4 | ENST00000261937.11 | c.633A>G | p.Gly211= | synonymous_variant | 5/30 | 1 | NM_182925.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0228 AC: 3469AN: 152162Hom.: 133 Cov.: 33
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GnomAD3 exomes AF: 0.00921 AC: 2301AN: 249906Hom.: 61 AF XY: 0.00863 AC XY: 1171AN XY: 135646
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GnomAD4 exome AF: 0.00393 AC: 5737AN: 1460550Hom.: 160 Cov.: 38 AF XY: 0.00432 AC XY: 3142AN XY: 726554
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GnomAD4 genome ? AF: 0.0229 AC: 3480AN: 152280Hom.: 135 Cov.: 33 AF XY: 0.0224 AC XY: 1671AN XY: 74446
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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 | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 13, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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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