1-109923833-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000757.6(CSF1):c.1212G>A(p.Arg404=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000312 in 1,613,632 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0019 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00015 ( 1 hom. )
Consequence
CSF1
NM_000757.6 synonymous
NM_000757.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0340
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 Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 1-109923833-G-A is Benign according to our data. Variant chr1-109923833-G-A is described in ClinVar as [Benign]. Clinvar id is 736032.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.034 with no splicing effect.
BS2
High AC in GnomAd4 at 289 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF1 | NM_000757.6 | c.1212G>A | p.Arg404= | synonymous_variant | 6/9 | ENST00000329608.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF1 | ENST00000329608.11 | c.1212G>A | p.Arg404= | synonymous_variant | 6/9 | 1 | NM_000757.6 | P4 | |
CSF1 | ENST00000369802.7 | c.1212G>A | p.Arg404= | synonymous_variant | 6/9 | 1 | P4 | ||
CSF1 | ENST00000369801.1 | c.1090+122G>A | intron_variant | 1 | |||||
CSF1 | ENST00000420111.6 | c.545-227G>A | intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00189 AC: 287AN: 152170Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000455 AC: 114AN: 250520Hom.: 1 AF XY: 0.000273 AC XY: 37AN XY: 135522
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GnomAD4 exome AF: 0.000146 AC: 214AN: 1461346Hom.: 1 Cov.: 77 AF XY: 0.000110 AC XY: 80AN XY: 726986
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GnomAD4 genome AF: 0.00190 AC: 289AN: 152286Hom.: 1 Cov.: 33 AF XY: 0.00180 AC XY: 134AN XY: 74464
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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 | Invitae | Jul 16, 2018 | - - |
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