chrX-49251390-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1BP6_ModerateBS2
The NM_014009.4(FOXP3):c.1240C>T(p.Arg414Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000678 in 1,209,894 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 36 hemizygotes in GnomAD. 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. R414H) has been classified as Likely benign.
Frequency
Consequence
NM_014009.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXP3 | NM_014009.4 | c.1240C>T | p.Arg414Cys | missense_variant | 12/12 | ENST00000376207.10 | |
FOXP3 | NM_001114377.2 | c.1135C>T | p.Arg379Cys | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXP3 | ENST00000376207.10 | c.1240C>T | p.Arg414Cys | missense_variant | 12/12 | 1 | NM_014009.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000446 AC: 5AN: 112204Hom.: 0 Cov.: 23 AF XY: 0.0000873 AC XY: 3AN XY: 34380
GnomAD3 exomes AF: 0.0000221 AC: 4AN: 180919Hom.: 0 AF XY: 0.0000456 AC XY: 3AN XY: 65737
GnomAD4 exome AF: 0.0000701 AC: 77AN: 1097690Hom.: 0 Cov.: 31 AF XY: 0.0000909 AC XY: 33AN XY: 363092
GnomAD4 genome ? AF: 0.0000446 AC: 5AN: 112204Hom.: 0 Cov.: 23 AF XY: 0.0000873 AC XY: 3AN XY: 34380
ClinVar
Submissions by phenotype
Insulin-dependent diabetes mellitus secretory diarrhea syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at