NM_001349338.3:c.*3399_*3414dupTGTGTGTGTGTGTGTG
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_001349338.3(FOXP1):c.*3399_*3414dupTGTGTGTGTGTGTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000126 in 221,632 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 0.000095 ( 0 hom., cov: 26)
Exomes 𝑓: 0.00019 ( 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 = 0.0000951 (14/147264) while in subpopulation EAS AF= 0.000598 (3/5016). AF 95% confidence interval is 0.000162. There are 0 homozygotes in gnomad4. There are 5 alleles in male gnomad4 subpopulation. Median coverage is 26. This position pass quality control queck.
BS2
High AC in GnomAd4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXP1 | NM_001349338.3 | c.*3399_*3414dupTGTGTGTGTGTGTGTG | 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.*3399_*3414dupTGTGTGTGTGTGTGTG | 3_prime_UTR_variant | Exon 21 of 21 | NM_001349338.3 | ENSP00000497369.1 | ||||
FOXP1 | ENST00000318789 | c.*3399_*3414dupTGTGTGTGTGTGTGTG | 3_prime_UTR_variant | Exon 21 of 21 | 1 | ENSP00000318902.5 |
Frequencies
GnomAD3 genomes AF: 0.0000951 AC: 14AN: 147168Hom.: 0 Cov.: 26
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GnomAD4 exome AF: 0.000188 AC: 14AN: 74368Hom.: 0 Cov.: 0 AF XY: 0.000205 AC XY: 7AN XY: 34160
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GnomAD4 genome AF: 0.0000951 AC: 14AN: 147264Hom.: 0 Cov.: 26 AF XY: 0.0000698 AC XY: 5AN XY: 71620
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at