chr1-36466461-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_000760.4(CSF3R):c.2407C>T(p.Pro803Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000279 in 1,612,292 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000760.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF3R | NM_000760.4 | c.2407C>T | p.Pro803Ser | missense_variant | 17/17 | ENST00000373106.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF3R | ENST00000373106.6 | c.2407C>T | p.Pro803Ser | missense_variant | 17/17 | 1 | NM_000760.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00171 AC: 261AN: 152220Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000324 AC: 79AN: 243918Hom.: 0 AF XY: 0.000226 AC XY: 30AN XY: 132482
GnomAD4 exome AF: 0.000129 AC: 189AN: 1459954Hom.: 2 Cov.: 31 AF XY: 0.000116 AC XY: 84AN XY: 726136
GnomAD4 genome ? AF: 0.00171 AC: 261AN: 152338Hom.: 1 Cov.: 32 AF XY: 0.00172 AC XY: 128AN XY: 74492
ClinVar
Submissions by phenotype
Autosomal recessive severe congenital neutropenia due to CSF3R deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
CSF3R-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 26, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at