rs146617729
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000760.4(CSF3R):c.2422G>A(p.Glu808Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00733 in 1,613,282 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E808G) has been classified as Uncertain significance.
Frequency
Consequence
NM_000760.4 missense
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 |
---|---|---|---|---|---|---|---|
CSF3R | NM_000760.4 | c.2422G>A | p.Glu808Lys | missense_variant | 17/17 | ENST00000373106.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF3R | ENST00000373106.6 | c.2422G>A | p.Glu808Lys | missense_variant | 17/17 | 1 | NM_000760.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00572 AC: 870AN: 152222Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00653 AC: 1618AN: 247678Hom.: 8 AF XY: 0.00646 AC XY: 868AN XY: 134298
GnomAD4 exome AF: 0.00750 AC: 10958AN: 1460942Hom.: 55 Cov.: 31 AF XY: 0.00732 AC XY: 5319AN XY: 726710
GnomAD4 genome ? AF: 0.00571 AC: 870AN: 152340Hom.: 2 Cov.: 32 AF XY: 0.00541 AC XY: 403AN XY: 74490
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 23, 2016 | - - |
Autosomal recessive severe congenital neutropenia due to CSF3R deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | CSF3R: BP4, BS1, BS2 - |
Hereditary neutrophilia;C4310764:Autosomal recessive severe congenital neutropenia due to CSF3R deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 02, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at