rs56960778
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000381500.6(CSF2RA):c.974G>A(p.Arg325His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000804 in 1,613,898 control chromosomes in the GnomAD database, including 5 homozygotes. There are 626 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R325C) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000381500.6 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 |
---|---|---|---|---|---|---|---|
CSF2RA | NM_172245.4 | c.1071G>A | p.Pro357= | synonymous_variant | 12/13 | ENST00000381529.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF2RA | ENST00000381529.9 | c.1071G>A | p.Pro357= | synonymous_variant | 12/13 | 1 | NM_172245.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00415 AC: 631AN: 152114Hom.: 2 Cov.: 32 AF XY: 0.00410 AC XY: 305AN XY: 74300
GnomAD3 exomes AF: 0.00107 AC: 270AN: 251168Hom.: 1 AF XY: 0.000781 AC XY: 106AN XY: 135738
GnomAD4 exome AF: 0.000454 AC: 664AN: 1461666Hom.: 3 Cov.: 32 AF XY: 0.000440 AC XY: 320AN XY: 727142
GnomAD4 genome ? AF: 0.00416 AC: 633AN: 152232Hom.: 2 Cov.: 32 AF XY: 0.00411 AC XY: 306AN XY: 74428
ClinVar
Submissions by phenotype
Surfactant metabolism dysfunction, pulmonary, 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
CSF2RA-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 13, 2019 | This variant is classified as 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