chr3-70955832-G-GCACACACACACACA
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_001349338.3(FOXP1):c.*3401_*3414dupTGTGTGTGTGTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000871 in 221,608 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00078 ( 0 hom., cov: 26)
Exomes 𝑓: 0.0010 ( 0 hom. )
Consequence
FOXP1
NM_001349338.3 3_prime_UTR
NM_001349338.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.373
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 Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000781 (115/147264) while in subpopulation EAS AF= 0.00279 (14/5016). AF 95% confidence interval is 0.00169. There are 0 homozygotes in gnomad4. There are 58 alleles in male gnomad4 subpopulation. Median coverage is 26. This position pass quality control queck.
BS2
High AC in GnomAd4 at 115 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXP1 | NM_001349338.3 | c.*3401_*3414dupTGTGTGTGTGTGTG | 3_prime_UTR_variant | Exon 21 of 21 | ENST00000649528.3 | NP_001336267.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXP1 | ENST00000649528 | c.*3401_*3414dupTGTGTGTGTGTGTG | 3_prime_UTR_variant | Exon 21 of 21 | NM_001349338.3 | ENSP00000497369.1 | ||||
FOXP1 | ENST00000318789 | c.*3401_*3414dupTGTGTGTGTGTGTG | 3_prime_UTR_variant | Exon 21 of 21 | 1 | ENSP00000318902.5 |
Frequencies
GnomAD3 genomes AF: 0.000775 AC: 114AN: 147168Hom.: 0 Cov.: 26
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GnomAD4 exome AF: 0.00105 AC: 78AN: 74344Hom.: 0 Cov.: 0 AF XY: 0.000966 AC XY: 33AN XY: 34146
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GnomAD4 genome AF: 0.000781 AC: 115AN: 147264Hom.: 0 Cov.: 26 AF XY: 0.000810 AC XY: 58AN XY: 71620
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at