5-180603221-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_182925.5(FLT4):c.4063G>A(p.Val1355Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000899 in 1,614,070 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_182925.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00158 AC: 240AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00137 AC: 343AN: 249466Hom.: 0 AF XY: 0.00120 AC XY: 162AN XY: 135256
GnomAD4 exome AF: 0.000828 AC: 1211AN: 1461700Hom.: 4 Cov.: 31 AF XY: 0.000802 AC XY: 583AN XY: 727170
GnomAD4 genome AF: 0.00158 AC: 240AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.00154 AC XY: 115AN XY: 74514
ClinVar
Submissions by phenotype
FLT4-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at