NM_000757.6:c.1095C>A
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_000757.6(CSF1):c.1095C>A(p.Thr365Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 1,612,420 control chromosomes in the GnomAD database, including 279,656 homozygotes. 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: 𝑓 0.48 ( 20144 hom., cov: 33)
Exomes 𝑓: 0.59 ( 259512 hom. )
Consequence
CSF1
NM_000757.6 synonymous
NM_000757.6 synonymous
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 Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP7
Synonymous conserved (PhyloP=-0.402 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSF1 | NM_000757.6 | c.1095C>A | p.Thr365Thr | synonymous_variant | Exon 6 of 9 | ENST00000329608.11 | NP_000748.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSF1 | ENST00000329608.11 | c.1095C>A | p.Thr365Thr | synonymous_variant | Exon 6 of 9 | 1 | NM_000757.6 | ENSP00000327513.6 | ||
CSF1 | ENST00000369802.7 | c.1095C>A | p.Thr365Thr | synonymous_variant | Exon 6 of 9 | 1 | ENSP00000358817.3 | |||
CSF1 | ENST00000369801.1 | c.1090+5C>A | splice_region_variant, intron_variant | Intron 6 of 8 | 1 | ENSP00000358816.1 | ||||
CSF1 | ENST00000420111.6 | c.545-344C>A | intron_variant | Intron 5 of 8 | 5 | ENSP00000407317.2 |
Frequencies
GnomAD3 genomes AF: 0.481 AC: 73135AN: 151960Hom.: 20143 Cov.: 33
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GnomAD3 exomes AF: 0.567 AC: 141740AN: 250112Hom.: 41927 AF XY: 0.574 AC XY: 77594AN XY: 135144
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GnomAD4 exome AF: 0.591 AC: 862869AN: 1460344Hom.: 259512 Cov.: 73 AF XY: 0.592 AC XY: 430328AN XY: 726316
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GnomAD4 genome AF: 0.481 AC: 73143AN: 152076Hom.: 20144 Cov.: 33 AF XY: 0.483 AC XY: 35898AN XY: 74344
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Not reported inComputational scores
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Name
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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