rs76714703
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001244753.2(FCGR3B):āc.194A>Gā(p.Asn65Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.92 ( 32445 hom., cov: 11)
Exomes š: 0.70 ( 337108 hom. )
Failed GnomAD Quality Control
Consequence
FCGR3B
NM_001244753.2 missense
NM_001244753.2 missense
Scores
11
Clinical Significance
Conservation
PhyloP100: -4.37
Genes affected
FCGR3B (HGNC:3620): (Fc gamma receptor IIIb) The protein encoded by this gene is a low affinity receptor for the Fc region of gamma immunoglobulins (IgG). The encoded protein acts as a monomer and can bind either monomeric or aggregated IgG. This gene may function to capture immune complexes in the peripheral circulation. Several transcript variants encoding different isoforms have been found for this gene. A highly-similar gene encoding a related protein is also found on chromosome 1. [provided by RefSeq, Aug 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=1.3109584E-6).
BP6
?
Variant 1-161629903-T-C is Benign according to our data. Variant chr1-161629903-T-C is described in ClinVar as [Benign]. Clinvar id is 242685.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-161629903-T-C is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCGR3B | NM_001244753.2 | c.194A>G | p.Asn65Ser | missense_variant | 3/5 | ENST00000650385.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCGR3B | ENST00000650385.1 | c.194A>G | p.Asn65Ser | missense_variant | 3/5 | NM_001244753.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.923 AC: 68982AN: 74730Hom.: 32429 Cov.: 11
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GnomAD3 exomes AF: 0.619 AC: 144438AN: 233468Hom.: 48541 AF XY: 0.624 AC XY: 79224AN XY: 127038
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.697 AC: 907130AN: 1300890Hom.: 337108 Cov.: 47 AF XY: 0.700 AC XY: 454087AN XY: 648784
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.923 AC: 69021AN: 74782Hom.: 32445 Cov.: 11 AF XY: 0.924 AC XY: 32691AN XY: 35374
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 26, 2017 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P;P;P;P;P
PrimateAI
Benign
T
Vest4
0.039, 0.037, 0.031, 0.034
MPC
1.4
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at