rs3829987
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001288705.3(CSF1R):c.889+28C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 1,613,674 control chromosomes in the GnomAD database, including 8,484 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.14 ( 3060 hom., cov: 32)
Exomes 𝑓: 0.051 ( 5424 hom. )
Consequence
CSF1R
NM_001288705.3 intron
NM_001288705.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.02
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
?
Variant 5-150077248-G-A is Benign according to our data. Variant chr5-150077248-G-A is described in ClinVar as [Benign]. Clinvar id is 1239548.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF1R | NM_001288705.3 | c.889+28C>T | intron_variant | ENST00000675795.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF1R | ENST00000675795.1 | c.889+28C>T | intron_variant | NM_001288705.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.143 AC: 21764AN: 152010Hom.: 3047 Cov.: 32
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GnomAD3 exomes AF: 0.101 AC: 25309AN: 251444Hom.: 2763 AF XY: 0.0861 AC XY: 11696AN XY: 135914
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GnomAD4 exome AF: 0.0513 AC: 75025AN: 1461546Hom.: 5424 Cov.: 32 AF XY: 0.0494 AC XY: 35942AN XY: 727096
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GnomAD4 genome ? AF: 0.143 AC: 21824AN: 152128Hom.: 3060 Cov.: 32 AF XY: 0.144 AC XY: 10696AN XY: 74368
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 10, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at