chr5-132075767-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000758.4(CSF2):āc.350T>Cā(p.Ile117Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,607,090 control chromosomes in the GnomAD database, including 47,794 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000758.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSF2 | NM_000758.4 | c.350T>C | p.Ile117Thr | missense_variant | 4/4 | ENST00000296871.4 | NP_000749.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSF2 | ENST00000296871.4 | c.350T>C | p.Ile117Thr | missense_variant | 4/4 | 1 | NM_000758.4 | ENSP00000296871.2 |
Frequencies
GnomAD3 genomes AF: 0.262 AC: 39826AN: 152022Hom.: 5817 Cov.: 33
GnomAD3 exomes AF: 0.265 AC: 65402AN: 247098Hom.: 10131 AF XY: 0.258 AC XY: 34537AN XY: 133938
GnomAD4 exome AF: 0.228 AC: 331618AN: 1454950Hom.: 41973 Cov.: 31 AF XY: 0.228 AC XY: 164856AN XY: 724190
GnomAD4 genome AF: 0.262 AC: 39843AN: 152140Hom.: 5821 Cov.: 33 AF XY: 0.269 AC XY: 19975AN XY: 74376
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at