rs2066933
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001288705.3(CSF1R):c.*35C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 1,604,874 control chromosomes in the GnomAD database, including 477,231 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.82 ( 51049 hom., cov: 31)
Exomes 𝑓: 0.76 ( 426182 hom. )
Consequence
CSF1R
NM_001288705.3 3_prime_UTR
NM_001288705.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.245
Genes affected
CSF1R (HGNC:2433): (colony stimulating factor 1 receptor) The protein encoded by this gene is the receptor for colony stimulating factor 1, a cytokine which controls the production, differentiation, and function of macrophages. This receptor mediates most if not all of the biological effects of this cytokine. Ligand binding activates the receptor kinase through a process of oligomerization and transphosphorylation. The encoded protein is a tyrosine kinase transmembrane receptor and member of the CSF1/PDGF receptor family of tyrosine-protein kinases. Mutations in this gene have been associated with a predisposition to myeloid malignancy. The first intron of this gene contains a transcriptionally inactive ribosomal protein L7 processed pseudogene oriented in the opposite direction. Alternative splicing results in multiple transcript variants. Expression of a splice variant from an LTR promoter has been found in Hodgkin lymphoma (HL), HL cell lines and anaplastic large cell lymphoma. [provided by RefSeq, Mar 2017]
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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=-0.91).
BP6
?
Variant 5-150054034-G-A is Benign according to our data. Variant chr5-150054034-G-A is described in ClinVar as [Benign]. Clinvar id is 352121.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF1R | NM_001288705.3 | c.*35C>T | 3_prime_UTR_variant | 21/21 | ENST00000675795.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF1R | ENST00000675795.1 | c.*35C>T | 3_prime_UTR_variant | 21/21 | NM_001288705.3 | P1 | |||
CSF1R | ENST00000286301.7 | c.*35C>T | 3_prime_UTR_variant | 22/22 | 1 | P1 | |||
CSF1R | ENST00000504875.5 | c.*775C>T | 3_prime_UTR_variant, NMD_transcript_variant | 20/20 | 1 | ||||
CSF1R | ENST00000509861.1 | n.690C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.816 AC: 123688AN: 151578Hom.: 50998 Cov.: 31
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GnomAD3 exomes AF: 0.769 AC: 188046AN: 244396Hom.: 72778 AF XY: 0.760 AC XY: 100516AN XY: 132184
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GnomAD4 exome AF: 0.764 AC: 1110901AN: 1453174Hom.: 426182 Cov.: 30 AF XY: 0.761 AC XY: 550281AN XY: 722938
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GnomAD4 genome ? AF: 0.816 AC: 123793AN: 151700Hom.: 51049 Cov.: 31 AF XY: 0.815 AC XY: 60384AN XY: 74124
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Hereditary diffuse leukoencephalopathy with spheroids Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 10, 2021 | - - |
Brain abnormalities, neurodegeneration, and dysosteosclerosis Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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