rs10079250
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001288705.3(CSF1R):āc.1085A>Gā(p.His362Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0797 in 1,520,942 control chromosomes in the GnomAD database, including 6,662 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H362C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001288705.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF1R | NM_001288705.3 | c.1085A>G | p.His362Arg | missense_variant, splice_region_variant | 7/21 | ENST00000675795.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF1R | ENST00000675795.1 | c.1085A>G | p.His362Arg | missense_variant, splice_region_variant | 7/21 | NM_001288705.3 | P1 | ||
CSF1R | ENST00000286301.7 | c.1085A>G | p.His362Arg | missense_variant, splice_region_variant | 8/22 | 1 | P1 | ||
CSF1R | ENST00000543093.1 | c.892A>G | p.Thr298Ala | missense_variant, splice_region_variant | 6/6 | 1 | |||
CSF1R | ENST00000504875.5 | c.1085A>G | p.His362Arg | missense_variant, splice_region_variant, NMD_transcript_variant | 7/20 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0889 AC: 13519AN: 152102Hom.: 880 Cov.: 32
GnomAD3 exomes AF: 0.0989 AC: 12544AN: 126780Hom.: 1133 AF XY: 0.101 AC XY: 6567AN XY: 65256
GnomAD4 exome AF: 0.0787 AC: 107721AN: 1368722Hom.: 5784 Cov.: 32 AF XY: 0.0797 AC XY: 53671AN XY: 673046
GnomAD4 genome ? AF: 0.0888 AC: 13522AN: 152220Hom.: 878 Cov.: 32 AF XY: 0.0877 AC XY: 6526AN XY: 74432
ClinVar
Submissions by phenotype
Hereditary diffuse leukoencephalopathy with spheroids Benign:3
Benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Sep 21, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 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, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | Dec 22, 2014 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | This variant is associated with the following publications: (PMID: 31182772, 30136118, 28724665, 25144241) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at