3-70955524-GA-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2
The NM_001349338.3(FOXP1):c.*3722del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000621 in 225,478 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000048 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000089 ( 0 hom. )
Consequence
FOXP1
NM_001349338.3 3_prime_UTR
NM_001349338.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.909
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 eas. gnomad4 allele frequency = 0.0000476 (7/146970) while in subpopulation EAS AF= 0.0004 (2/4998). AF 95% confidence interval is 0.0000706. There are 0 homozygotes in gnomad4. There are 2 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
?
High AC in GnomAd at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXP1 | NM_001349338.3 | c.*3722del | 3_prime_UTR_variant | 21/21 | ENST00000649528.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXP1 | ENST00000649528.3 | c.*3722del | 3_prime_UTR_variant | 21/21 | NM_001349338.3 | P4 | |||
FOXP1 | ENST00000318789.11 | c.*3722del | 3_prime_UTR_variant | 21/21 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000476 AC: 7AN: 146926Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000892 AC: 7AN: 78508Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 36142
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GnomAD4 genome ? AF: 0.0000476 AC: 7AN: 146970Hom.: 0 Cov.: 32 AF XY: 0.0000280 AC XY: 2AN XY: 71398
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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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Find out detailed SpliceAI scores and Pangolin per-transcript scores at