chrX-1282715-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_172245.4(CSF2RA):c.12G>C(p.Leu4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,406 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L4L) has been classified as Likely benign.
Frequency
Consequence
NM_172245.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF2RA | NM_172245.4 | c.12G>C | p.Leu4= | synonymous_variant | 3/13 | ENST00000381529.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF2RA | ENST00000381529.9 | c.12G>C | p.Leu4= | synonymous_variant | 3/13 | 1 | NM_172245.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152054Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74278
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251180Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135744
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461352Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727002
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152054Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74278
ClinVar
Submissions by phenotype
Surfactant metabolism dysfunction, pulmonary, 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at