chr3-70956489-G-GT
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2
The NM_001349338.3(FOXP1):c.*2757_*2758insA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00295 in 207,190 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00036 ( 0 hom., cov: 29)
Exomes 𝑓: 0.0087 ( 0 hom. )
Consequence
FOXP1
NM_001349338.3 3_prime_UTR
NM_001349338.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.48
Genes affected
FOXP1 (HGNC:3823): (forkhead box P1) This gene belongs to subfamily P of the forkhead box (FOX) transcription factor family. Forkhead box transcription factors play important roles in the regulation of tissue- and cell type-specific gene transcription during both development and adulthood. Forkhead box P1 protein contains both DNA-binding- and protein-protein binding-domains. This gene may act as a tumor suppressor as it is lost in several tumor types and maps to a chromosomal region (3p14.1) reported to contain a tumor suppressor gene(s). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000364 (52/142722) while in subpopulation AFR AF= 0.000846 (33/39010). AF 95% confidence interval is 0.000619. There are 0 homozygotes in gnomad4. There are 28 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High AC in GnomAd4 at 52 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXP1 | NM_001349338.3 | c.*2757_*2758insA | 3_prime_UTR_variant | 21/21 | ENST00000649528.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXP1 | ENST00000649528.3 | c.*2757_*2758insA | 3_prime_UTR_variant | 21/21 | NM_001349338.3 | P4 | |||
FOXP1 | ENST00000318789.11 | c.*2757_*2758insA | 3_prime_UTR_variant | 21/21 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000365 AC: 52AN: 142632Hom.: 0 Cov.: 29
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GnomAD4 exome AF: 0.00869 AC: 560AN: 64468Hom.: 0 Cov.: 0 AF XY: 0.00802 AC XY: 238AN XY: 29674
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GnomAD4 genome AF: 0.000364 AC: 52AN: 142722Hom.: 0 Cov.: 29 AF XY: 0.000404 AC XY: 28AN XY: 69298
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Intellectual Disability with Language Impairment and Autistic Features Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at