rs2232368
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014009.4(FOXP3):c.648-20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0188 in 1,177,354 control chromosomes in the GnomAD database, including 244 homozygotes. There are 6,819 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.014 ( 18 hom., 454 hem., cov: 23)
Exomes 𝑓: 0.019 ( 226 hom. 6365 hem. )
Consequence
FOXP3
NM_014009.4 intron
NM_014009.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.366
Genes affected
FOXP3 (HGNC:6106): (forkhead box P3) The protein encoded by this gene is a member of the forkhead/winged-helix family of transcriptional regulators. Defects in this gene are the cause of immunodeficiency polyendocrinopathy, enteropathy, X-linked syndrome (IPEX), also known as X-linked autoimmunity-immunodeficiency syndrome. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant X-49255822-C-T is Benign according to our data. Variant chrX-49255822-C-T is described in ClinVar as [Benign]. Clinvar id is 1170241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0779 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXP3 | NM_014009.4 | c.648-20G>A | intron_variant | ENST00000376207.10 | |||
FOXP3 | NM_001114377.2 | c.543-20G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXP3 | ENST00000376207.10 | c.648-20G>A | intron_variant | 1 | NM_014009.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0143 AC: 1596AN: 111837Hom.: 17 Cov.: 23 AF XY: 0.0133 AC XY: 452AN XY: 34015
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GnomAD3 exomes AF: 0.0232 AC: 3640AN: 156851Hom.: 80 AF XY: 0.0197 AC XY: 953AN XY: 48485
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GnomAD4 exome AF: 0.0192 AC: 20480AN: 1065464Hom.: 226 Cov.: 28 AF XY: 0.0190 AC XY: 6365AN XY: 334816
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GnomAD4 genome ? AF: 0.0143 AC: 1604AN: 111890Hom.: 18 Cov.: 23 AF XY: 0.0133 AC XY: 454AN XY: 34078
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Insulin-dependent diabetes mellitus secretory diarrhea syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 11, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 20, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at