chrX-1288840-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_172245.4(CSF2RA):c.425C>T(p.Pro142Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00245 in 1,613,894 control chromosomes in the GnomAD database, including 87 homozygotes. There are 1,737 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_172245.4 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: 0.0125 AC: 1904AN: 152124Hom.: 40 Cov.: 32 AF XY: 0.0119 AC XY: 885AN XY: 74312
GnomAD3 exomes AF: 0.00336 AC: 843AN: 251094Hom.: 19 AF XY: 0.00231 AC XY: 313AN XY: 135734
GnomAD4 exome AF: 0.00140 AC: 2040AN: 1461652Hom.: 47 Cov.: 34 AF XY: 0.00117 AC XY: 848AN XY: 727138
GnomAD4 genome AF: 0.0125 AC: 1907AN: 152242Hom.: 40 Cov.: 32 AF XY: 0.0119 AC XY: 889AN XY: 74440
ClinVar
Submissions by phenotype
Surfactant metabolism dysfunction, pulmonary, 4 Benign:2
Benign, criteria provided, single submitter | clinical testing | Johns Hopkins Genomics, Johns Hopkins University | Mar 05, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 27, 2025 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 05, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 21, 2013 | Pro142Leu in exon 7 of CSF2RA: This variant is not expected to have clinical sig nificance because it has been identified in 4.8% (210/4406) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs151058706). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at