rs138964358
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_172245.4(CSF2RA):c.491G>A(p.Arg164Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00776 in 1,613,084 control chromosomes in the GnomAD database, including 71 homozygotes. There are 6,063 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R164W) 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 -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF2RA | NM_172245.4 | c.491G>A | p.Arg164Gln | missense_variant | 7/13 | ENST00000381529.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF2RA | ENST00000381529.9 | c.491G>A | p.Arg164Gln | missense_variant | 7/13 | 1 | NM_172245.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00534 AC: 811AN: 151886Hom.: 2 Cov.: 31 AF XY: 0.00492 AC XY: 365AN XY: 74172
GnomAD3 exomes AF: 0.00512 AC: 1285AN: 251150Hom.: 8 AF XY: 0.00497 AC XY: 675AN XY: 135728
GnomAD4 exome AF: 0.00801 AC: 11705AN: 1461086Hom.: 69 Cov.: 32 AF XY: 0.00784 AC XY: 5698AN XY: 726852
GnomAD4 genome ? AF: 0.00532 AC: 809AN: 151998Hom.: 2 Cov.: 31 AF XY: 0.00491 AC XY: 365AN XY: 74294
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 21, 2013 | Arg164Gln in exon 8 of CSF2RA: This variant is not expected to have clinical sig nificance because it has been identified in 0.8% (66/8592) of European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs138964358). - |
Surfactant metabolism dysfunction, pulmonary, 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at