rs372852278
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_172245.4(CSF2RA):āc.972T>Gā(p.Ser324=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,613,624 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 34 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. S324S) 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 -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF2RA | NM_172245.4 | c.972T>G | p.Ser324= | synonymous_variant | 11/13 | ENST00000381529.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF2RA | ENST00000381529.9 | c.972T>G | p.Ser324= | synonymous_variant | 11/13 | 1 | NM_172245.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000244 AC: 37AN: 151874Hom.: 0 Cov.: 31 AF XY: 0.000229 AC XY: 17AN XY: 74138
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251180Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135744
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461632Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 727124
GnomAD4 genome ? AF: 0.000243 AC: 37AN: 151992Hom.: 0 Cov.: 31 AF XY: 0.000229 AC XY: 17AN XY: 74266
ClinVar
Submissions by phenotype
Surfactant metabolism dysfunction, pulmonary, 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 16, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at