rs200554980
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_014009.4(FOXP3):c.340C>T(p.Arg114Trp) variant causes a missense change. The variant allele was found at a frequency of 0.000168 in 1,179,256 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 62 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R114Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_014009.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXP3 | NM_014009.4 | c.340C>T | p.Arg114Trp | missense_variant | 4/12 | ENST00000376207.10 | |
FOXP3 | NM_001114377.2 | c.235C>T | p.Arg79Trp | missense_variant | 3/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXP3 | ENST00000376207.10 | c.340C>T | p.Arg114Trp | missense_variant | 4/12 | 1 | NM_014009.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000214 AC: 24AN: 111987Hom.: 0 Cov.: 23 AF XY: 0.000322 AC XY: 11AN XY: 34187
GnomAD3 exomes AF: 0.000264 AC: 41AN: 155102Hom.: 0 AF XY: 0.000309 AC XY: 15AN XY: 48538
GnomAD4 exome AF: 0.000163 AC: 174AN: 1067269Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 51AN XY: 343677
GnomAD4 genome ? AF: 0.000214 AC: 24AN: 111987Hom.: 0 Cov.: 23 AF XY: 0.000322 AC XY: 11AN XY: 34187
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 03, 2016 | - - |
Insulin-dependent diabetes mellitus secretory diarrhea syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at