chr3-70955638-T-TA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001349338.3(FOXP1):c.*3608_*3609insT variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.00389 in 233,496 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0036 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0045 ( 1 hom. )
Consequence
FOXP1
NM_001349338.3 3_prime_UTR
NM_001349338.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.31
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 -10 ACMG points.
BP6
?
Variant 3-70955638-T-TA is Benign according to our data. Variant chr3-70955638-T-TA is described in ClinVar as [Likely_benign]. Clinvar id is 346556.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00358 (545/152194) while in subpopulation SAS AF= 0.0147 (71/4818). AF 95% confidence interval is 0.012. There are 4 homozygotes in gnomad4. There are 276 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 546 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXP1 | NM_001349338.3 | c.*3608_*3609insT | 3_prime_UTR_variant | 21/21 | ENST00000649528.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXP1 | ENST00000649528.3 | c.*3608_*3609insT | 3_prime_UTR_variant | 21/21 | NM_001349338.3 | P4 | |||
FOXP1 | ENST00000318789.11 | c.*3608_*3609insT | 3_prime_UTR_variant | 21/21 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00359 AC: 546AN: 152076Hom.: 4 Cov.: 32
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GnomAD4 exome AF: 0.00448 AC: 364AN: 81302Hom.: 1 Cov.: 0 AF XY: 0.00489 AC XY: 183AN XY: 37416
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GnomAD4 genome ? AF: 0.00358 AC: 545AN: 152194Hom.: 4 Cov.: 32 AF XY: 0.00371 AC XY: 276AN XY: 74416
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Intellectual Disability with Language Impairment and Autistic Features Benign:1
Likely benign, 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