chrX-49250661-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014009.4(FOXP3):c.*673G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0047 in 281,687 control chromosomes in the GnomAD database, including 16 homozygotes. There are 357 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0086 ( 12 hom., 262 hem., cov: 24)
Exomes 𝑓: 0.0021 ( 4 hom. 95 hem. )
Consequence
FOXP3
NM_014009.4 3_prime_UTR
NM_014009.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.02
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=-0.94).
BP6
Variant X-49250661-C-T is Benign according to our data. Variant chrX-49250661-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 260313.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00864 (970/112312) while in subpopulation AFR AF= 0.0276 (853/30901). AF 95% confidence interval is 0.0261. There are 12 homozygotes in gnomad4. There are 262 alleles in male gnomad4 subpopulation. Median coverage is 24. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 12 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXP3 | NM_014009.4 | c.*673G>A | 3_prime_UTR_variant | 12/12 | ENST00000376207.10 | NP_054728.2 | ||
FOXP3 | NM_001114377.2 | c.*673G>A | 3_prime_UTR_variant | 11/11 | NP_001107849.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXP3 | ENST00000376207.10 | c.*673G>A | 3_prime_UTR_variant | 12/12 | 1 | NM_014009.4 | ENSP00000365380 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00860 AC: 965AN: 112258Hom.: 12 Cov.: 24 AF XY: 0.00755 AC XY: 260AN XY: 34454
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GnomAD4 exome AF: 0.00210 AC: 355AN: 169375Hom.: 4 Cov.: 0 AF XY: 0.00169 AC XY: 95AN XY: 56069
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GnomAD4 genome AF: 0.00864 AC: 970AN: 112312Hom.: 12 Cov.: 24 AF XY: 0.00759 AC XY: 262AN XY: 34518
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at