1-109923716-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000369801.1(CSF1):c.1090+5C>G variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Consequence
CSF1
ENST00000369801.1 splice_donor_5th_base, intron
ENST00000369801.1 splice_donor_5th_base, intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.402
Genes affected
CSF1 (HGNC:2432): (colony stimulating factor 1) The protein encoded by this gene is a cytokine that controls the production, differentiation, and function of macrophages. The active form of the protein is found extracellularly as a disulfide-linked homodimer, and is thought to be produced by proteolytic cleavage of membrane-bound precursors. The encoded protein may be involved in development of the placenta. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF1 | NM_000757.6 | c.1095C>G | p.Thr365= | synonymous_variant | 6/9 | ENST00000329608.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF1 | ENST00000329608.11 | c.1095C>G | p.Thr365= | synonymous_variant | 6/9 | 1 | NM_000757.6 | P4 | |
CSF1 | ENST00000369802.7 | c.1095C>G | p.Thr365= | synonymous_variant | 6/9 | 1 | P4 | ||
CSF1 | ENST00000369801.1 | c.1090+5C>G | splice_donor_5th_base_variant, intron_variant | 1 | |||||
CSF1 | ENST00000420111.6 | c.545-344C>G | intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 73
GnomAD4 exome
Cov.:
73
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -5
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.