5-180603322-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_182925.5(FLT4):c.3962G>A(p.Arg1321Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 1,612,680 control chromosomes in the GnomAD database, including 192 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_182925.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FLT4 | NM_182925.5 | c.3962G>A | p.Arg1321Gln | missense_variant | 30/30 | ENST00000261937.11 | NP_891555.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLT4 | ENST00000261937.11 | c.3962G>A | p.Arg1321Gln | missense_variant | 30/30 | 1 | NM_182925.5 | ENSP00000261937.6 | ||
FLT4 | ENST00000502603.5 | n.662G>A | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00929 AC: 1414AN: 152242Hom.: 14 Cov.: 33
GnomAD3 exomes AF: 0.00891 AC: 2201AN: 247058Hom.: 17 AF XY: 0.00876 AC XY: 1175AN XY: 134092
GnomAD4 exome AF: 0.0146 AC: 21327AN: 1460320Hom.: 178 Cov.: 32 AF XY: 0.0142 AC XY: 10333AN XY: 726496
GnomAD4 genome AF: 0.00927 AC: 1412AN: 152360Hom.: 14 Cov.: 33 AF XY: 0.00858 AC XY: 639AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 20, 2023 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at