rs782239006
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_014009.4(FOXP3):c.112G>T(p.Ala38Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000372 in 1,170,522 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 125 hemizygotes in GnomAD. 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 Benign (★).
Frequency
Consequence
NM_014009.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXP3 | NM_014009.4 | c.112G>T | p.Ala38Ser | missense_variant | 2/12 | ENST00000376207.10 | |
FOXP3 | NM_001114377.2 | c.112G>T | p.Ala38Ser | missense_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXP3 | ENST00000376207.10 | c.112G>T | p.Ala38Ser | missense_variant | 2/12 | 1 | NM_014009.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000444 AC: 5AN: 112688Hom.: 0 Cov.: 24 AF XY: 0.0000287 AC XY: 1AN XY: 34846
GnomAD3 exomes AF: 0.0000506 AC: 6AN: 118541Hom.: 0 AF XY: 0.0000497 AC XY: 2AN XY: 40265
GnomAD4 exome AF: 0.000407 AC: 431AN: 1057834Hom.: 0 Cov.: 30 AF XY: 0.000360 AC XY: 124AN XY: 344716
GnomAD4 genome ? AF: 0.0000444 AC: 5AN: 112688Hom.: 0 Cov.: 24 AF XY: 0.0000287 AC XY: 1AN XY: 34846
ClinVar
Submissions by phenotype
Insulin-dependent diabetes mellitus secretory diarrhea syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at