rs140060227
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001349338.3(FOXP1):c.1146+19C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000386 in 1,609,652 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0021 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00020 ( 2 hom. )
Consequence
FOXP1
NM_001349338.3 intron
NM_001349338.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.368
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 3-70987975-G-C is Benign according to our data. Variant chr3-70987975-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 445566.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 = 0.00213 (324/152228) while in subpopulation AFR AF= 0.00752 (312/41496). AF 95% confidence interval is 0.00683. There are 0 homozygotes in gnomad4. There are 162 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 324 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXP1 | NM_001349338.3 | c.1146+19C>G | intron_variant | ENST00000649528.3 | NP_001336267.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXP1 | ENST00000649528.3 | c.1146+19C>G | intron_variant | NM_001349338.3 | ENSP00000497369 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00212 AC: 322AN: 152110Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000581 AC: 146AN: 251134Hom.: 0 AF XY: 0.000412 AC XY: 56AN XY: 135762
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GnomAD4 exome AF: 0.000204 AC: 298AN: 1457424Hom.: 2 Cov.: 30 AF XY: 0.000152 AC XY: 110AN XY: 725250
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GnomAD4 genome AF: 0.00213 AC: 324AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.00218 AC XY: 162AN XY: 74432
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 24, 2017 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at