chr1-161673133-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001394477.1(FCGR2B):c.550C>T(p.Pro184Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001394477.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FCGR2B | NM_001394477.1 | c.550C>T | p.Pro184Ser | missense_variant | Exon 4 of 8 | ENST00000358671.10 | NP_001381406.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 8AN: 151586Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000891 AC: 13AN: 1458950Hom.: 0 Cov.: 30 AF XY: 0.00000689 AC XY: 5AN XY: 725644
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000527 AC: 8AN: 151704Hom.: 0 Cov.: 32 AF XY: 0.0000540 AC XY: 4AN XY: 74136
ClinVar
Submissions by phenotype
not provided Uncertain:1
The FCGR2B p.Pro184Ser variant was not identified in the literature nor was it identified in ClinVar. The variant was identified in dbSNP (ID: rs772853792). The variant was identified in control databases in 2 of 276584 chromosomes at a frequency of 0.000007231 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Other in 1 of 7080 chromosomes (freq: 0.000141), European (non-Finnish) in 1 of 126220 chromosomes (freq: 0.000008), but was not observed in the African, Latino, Ashkenazi Jewish, East Asian, European (Finnish), or South Asian populations. The p.Pro184 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at