rs112441738
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_172245.4(CSF2RA):c.540G>A(p.Leu180=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000209 in 1,613,620 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 145 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L180L) has been classified as Likely benign.
Frequency
Consequence
NM_172245.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF2RA | NM_172245.4 | c.540G>A | p.Leu180= | synonymous_variant | 7/13 | ENST00000381529.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF2RA | ENST00000381529.9 | c.540G>A | p.Leu180= | synonymous_variant | 7/13 | 1 | NM_172245.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00109 AC: 166AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.00108 AC XY: 80AN XY: 74286
GnomAD3 exomes AF: 0.000330 AC: 83AN: 251178Hom.: 0 AF XY: 0.000265 AC XY: 36AN XY: 135742
GnomAD4 exome AF: 0.000118 AC: 172AN: 1461422Hom.: 0 Cov.: 32 AF XY: 0.0000894 AC XY: 65AN XY: 727034
GnomAD4 genome ? AF: 0.00108 AC: 165AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.00108 AC XY: 80AN XY: 74414
ClinVar
Submissions by phenotype
Surfactant metabolism dysfunction, pulmonary, 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 30, 2023 | - - |
CSF2RA-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 24, 2023 | 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