chrX-1288578-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_172245.4(CSF2RA):āc.279A>Gā(p.Thr93=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00124 in 1,613,958 control chromosomes in the GnomAD database, including 6 homozygotes. There are 1,060 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. T93T) 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.279A>G | p.Thr93= | synonymous_variant | 5/13 | ENST00000381529.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF2RA | ENST00000381529.9 | c.279A>G | p.Thr93= | synonymous_variant | 5/13 | 1 | NM_172245.4 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00154 AC: 234AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.00165 AC XY: 123AN XY: 74340
GnomAD3 exomes AF: 0.00162 AC: 406AN: 251182Hom.: 0 AF XY: 0.00176 AC XY: 239AN XY: 135744
GnomAD4 exome AF: 0.00120 AC: 1761AN: 1461664Hom.: 6 Cov.: 33 AF XY: 0.00129 AC XY: 937AN XY: 727140
GnomAD4 genome AF: 0.00154 AC: 235AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.00165 AC XY: 123AN XY: 74468
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 | Sep 02, 2015 | p.Thr93Thr in exon 6 of CSF2RA: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue and is not located wi thin the splice consensus sequence. It has been identified in 0.1% (14/10406) of African chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broa dinstitute.org; dbSNP 140581875) - |
Surfactant metabolism dysfunction, pulmonary, 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at