rs760207183
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_172245.4(CSF2RA):c.1016G>T(p.Gly339Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 1,612,860 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 55 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G339S) has been classified as Uncertain significance.
Frequency
Consequence
NM_172245.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF2RA | NM_172245.4 | c.1016G>T | p.Gly339Val | missense_variant | 11/13 | ENST00000381529.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF2RA | ENST00000381529.9 | c.1016G>T | p.Gly339Val | missense_variant | 11/13 | 1 | NM_172245.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000264 AC: 4AN: 151230Hom.: 0 Cov.: 27 AF XY: 0.0000271 AC XY: 2AN XY: 73762
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251182Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135744
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1461630Hom.: 0 Cov.: 35 AF XY: 0.0000729 AC XY: 53AN XY: 727120
GnomAD4 genome ? AF: 0.0000264 AC: 4AN: 151230Hom.: 0 Cov.: 27 AF XY: 0.0000271 AC XY: 2AN XY: 73762
ClinVar
Submissions by phenotype
Surfactant metabolism dysfunction, pulmonary, 4 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 23, 2018 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with CSF2RA-related disease. This variant is present in population databases (rs760207183, ExAC 0.05%). This sequence change replaces glycine with valine at codon 339 of the CSF2RA protein (p.Gly339Val). The glycine residue is weakly conserved and there is a moderate physicochemical difference between glycine and valine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at