rs1801122
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000395.3(CSF2RB):c.1807C>A(p.Pro603Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.039 in 1,572,632 control chromosomes in the GnomAD database, including 1,340 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000395.3 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 |
---|---|---|---|---|---|---|---|
CSF2RB | NM_000395.3 | c.1807C>A | p.Pro603Thr | missense_variant | 14/14 | ENST00000403662.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF2RB | ENST00000403662.8 | c.1807C>A | p.Pro603Thr | missense_variant | 14/14 | 5 | NM_000395.3 | P1 | |
CSF2RB | ENST00000406230.5 | c.1825C>A | p.Pro609Thr | missense_variant | 13/13 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0301 AC: 4586AN: 152166Hom.: 101 Cov.: 32
GnomAD3 exomes AF: 0.0318 AC: 5679AN: 178744Hom.: 121 AF XY: 0.0334 AC XY: 3239AN XY: 96890
GnomAD4 exome AF: 0.0399 AC: 56717AN: 1420348Hom.: 1239 Cov.: 35 AF XY: 0.0399 AC XY: 28009AN XY: 702762
GnomAD4 genome ? AF: 0.0301 AC: 4587AN: 152284Hom.: 101 Cov.: 32 AF XY: 0.0304 AC XY: 2260AN XY: 74462
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | This variant is associated with the following publications: (PMID: 21205713, 20981092, 9410898, 27884173) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 26, 2014 | p.Pro603Thr in exon 14 of CSF2RB: This variant is not expected to have clinical significance because it has been identified in 3.6% (305/8368) of European Ameri can chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington. edu/EVS/; dbSNP rs1801122). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at