chr11-47358725-G-GCACACA
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The ENST00000533968.1(SPI1):c.606_611dupTGTGTG(p.Cys204_Met205insValCys) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000424 in 943,314 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 0.0000066 ( 0 hom., cov: 27)
Exomes 𝑓: 0.0000038 ( 0 hom. )
Consequence
SPI1
ENST00000533968.1 disruptive_inframe_insertion
ENST00000533968.1 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0410
Genes affected
SPI1 (HGNC:11241): (Spi-1 proto-oncogene) This gene encodes an ETS-domain transcription factor that activates gene expression during myeloid and B-lymphoid cell development. The nuclear protein binds to a purine-rich sequence known as the PU-box found near the promoters of target genes, and regulates their expression in coordination with other transcription factors and cofactors. The protein can also regulate alternative splicing of target genes. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in ENST00000533968.1.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPI1 | ENST00000533968.1 | c.606_611dupTGTGTG | p.Cys204_Met205insValCys | disruptive_inframe_insertion | Exon 4 of 4 | 1 | ENSP00000438846.1 | |||
SPI1 | ENST00000378538.8 | c.493+113_493+118dupTGTGTG | intron_variant | Intron 4 of 4 | 1 | NM_003120.3 | ENSP00000367799.4 | |||
SPI1 | ENST00000227163.8 | c.496+113_496+118dupTGTGTG | intron_variant | Intron 4 of 4 | 2 | ENSP00000227163.4 | ||||
SPI1 | ENST00000533030.1 | c.46-3185_46-3180dupTGTGTG | intron_variant | Intron 1 of 1 | 2 | ENSP00000443865.1 |
Frequencies
GnomAD3 genomes AF: 0.00000663 AC: 1AN: 150902Hom.: 0 Cov.: 27
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GnomAD3 exomes AF: 0.00000822 AC: 1AN: 121646Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 65788
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GnomAD4 exome AF: 0.00000379 AC: 3AN: 792412Hom.: 0 Cov.: 11 AF XY: 0.00000243 AC XY: 1AN XY: 411692
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GnomAD4 genome AF: 0.00000663 AC: 1AN: 150902Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 73598
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at