NM_172245.4:c.999G>A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_172245.4(CSF2RA):c.999G>A(p.Val333Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 1,611,098 control chromosomes in the GnomAD database, including 130,600 homozygotes. There are 318,614 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as 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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.369 AC: 55455AN: 150282Hom.: 10486 Cov.: 28 AF XY: 0.367 AC XY: 26873AN XY: 73154
GnomAD3 exomes AF: 0.373 AC: 93680AN: 251110Hom.: 17961 AF XY: 0.376 AC XY: 51008AN XY: 135690
GnomAD4 exome AF: 0.403 AC: 588155AN: 1460694Hom.: 120110 Cov.: 48 AF XY: 0.402 AC XY: 291723AN XY: 726492
GnomAD4 genome AF: 0.369 AC: 55464AN: 150404Hom.: 10490 Cov.: 28 AF XY: 0.367 AC XY: 26891AN XY: 73284
ClinVar
Submissions by phenotype
not provided Benign:2Other:1
Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
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not specified Benign:1
Val333Val in exon 12 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 43.0% (3695/8592) of European American chromosomes from a broad population by the NHLBI Exome Sequ encing Project (http://evs.gs.washington.edu/EVS; dbSNP rs146020675). -
Surfactant metabolism dysfunction, pulmonary, 4 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at