chrX-1309528-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000355432.8(CSF2RA):c.1073G>T(p.Arg358Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0843 in 1,613,540 control chromosomes in the GnomAD database, including 10,306 homozygotes. There are 71,282 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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R358Q) has been classified as Likely benign.
Frequency
Consequence
ENST00000355432.8 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.*49G>T | 3_prime_UTR_variant | 13/13 | ENST00000381529.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF2RA | ENST00000381529.9 | c.*49G>T | 3_prime_UTR_variant | 13/13 | 1 | NM_172245.4 | A2 |
Frequencies
GnomAD3 genomes AF: 0.144 AC: 21955AN: 152040Hom.: 2527 Cov.: 33 AF XY: 0.147 AC XY: 10885AN XY: 74270
GnomAD3 exomes AF: 0.113 AC: 28443AN: 251160Hom.: 2628 AF XY: 0.116 AC XY: 15770AN XY: 135722
GnomAD4 exome AF: 0.0780 AC: 113991AN: 1461382Hom.: 7764 Cov.: 33 AF XY: 0.0830 AC XY: 60353AN XY: 726962
GnomAD4 genome AF: 0.145 AC: 22006AN: 152158Hom.: 2542 Cov.: 33 AF XY: 0.147 AC XY: 10929AN XY: 74398
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 26, 2014 | p.Arg358Leu in exon 11 of CSF2RA: This variant is not expected to have clinical significance because it has been identified in 30% (1324/4406) of African Americ an chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.e du/EVS/; dbSNP rs28722602). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 06, 2019 | - - |
CSF2RA-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 03, 2020 | 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