X-1309528-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_172246.4(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 Benign (★★).
Frequency
Consequence
NM_172246.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
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 provided Benign:2
- -
- -
not specified Benign:1
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). -
CSF2RA-related disorder Benign:1
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