rs16846
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_000395.3(CSF2RB):c.702C>T(p.Cys234Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 1,613,734 control chromosomes in the GnomAD database, including 1,309 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000395.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSF2RB | ENST00000403662.8 | c.702C>T | p.Cys234Cys | synonymous_variant | Exon 6 of 14 | 5 | NM_000395.3 | ENSP00000384053.3 | ||
CSF2RB | ENST00000406230.5 | c.702C>T | p.Cys234Cys | synonymous_variant | Exon 5 of 13 | 1 | ENSP00000385271.1 | |||
CSF2RB | ENST00000421539.1 | c.462C>T | p.Cys154Cys | synonymous_variant | Exon 5 of 7 | 5 | ENSP00000393585.1 |
Frequencies
GnomAD3 genomes AF: 0.0455 AC: 6926AN: 152188Hom.: 193 Cov.: 32
GnomAD3 exomes AF: 0.0324 AC: 8058AN: 248422Hom.: 176 AF XY: 0.0325 AC XY: 4389AN XY: 134940
GnomAD4 exome AF: 0.0347 AC: 50686AN: 1461428Hom.: 1115 Cov.: 32 AF XY: 0.0348 AC XY: 25274AN XY: 727012
GnomAD4 genome AF: 0.0455 AC: 6935AN: 152306Hom.: 194 Cov.: 32 AF XY: 0.0441 AC XY: 3283AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
Cys234Cys in exon 6 of CSF2RB: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 8.0% (352/4406) of African American chromosomes from a broad population by the NHLBI Exome Sequenci ng Project (http://evs.gs.washington.edu/EVS; dbSNP rs16846). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at