chrX-49251389-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM1BP4BP6_Very_StrongBS2
The NM_014009.4(FOXP3):c.1241G>A(p.Arg414His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000122 in 1,209,860 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 42 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R414C) has been classified as Likely benign.
Frequency
Consequence
NM_014009.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXP3 | NM_014009.4 | c.1241G>A | p.Arg414His | missense_variant | 12/12 | ENST00000376207.10 | |
FOXP3 | NM_001114377.2 | c.1136G>A | p.Arg379His | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXP3 | ENST00000376207.10 | c.1241G>A | p.Arg414His | missense_variant | 12/12 | 1 | NM_014009.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000534 AC: 6AN: 112316Hom.: 0 Cov.: 22 AF XY: 0.0000290 AC XY: 1AN XY: 34476
GnomAD3 exomes AF: 0.0000664 AC: 12AN: 180641Hom.: 0 AF XY: 0.0000916 AC XY: 6AN XY: 65497
GnomAD4 exome AF: 0.000129 AC: 142AN: 1097544Hom.: 0 Cov.: 31 AF XY: 0.000113 AC XY: 41AN XY: 362950
GnomAD4 genome ? AF: 0.0000534 AC: 6AN: 112316Hom.: 0 Cov.: 22 AF XY: 0.0000290 AC XY: 1AN XY: 34476
ClinVar
Submissions by phenotype
Insulin-dependent diabetes mellitus secretory diarrhea syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 30, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at