rs10494360
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001136219.3(FCGR2A):c.86-27G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,611,998 control chromosomes in the GnomAD database, including 11,451 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.090 ( 866 hom., cov: 32)
Exomes 𝑓: 0.11 ( 10585 hom. )
Consequence
FCGR2A
NM_001136219.3 intron
NM_001136219.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.697
Genes affected
FCGR2A (HGNC:3616): (Fc gamma receptor IIa) This gene encodes one member of a family of immunoglobulin Fc receptor genes found on the surface of many immune response cells. The protein encoded by this gene is a cell surface receptor found on phagocytic cells such as macrophages and neutrophils, and is involved in the process of phagocytosis and clearing of immune complexes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCGR2A | NM_001136219.3 | c.86-27G>A | intron_variant | ENST00000271450.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCGR2A | ENST00000271450.12 | c.86-27G>A | intron_variant | 1 | NM_001136219.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0901 AC: 13702AN: 152130Hom.: 863 Cov.: 32
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GnomAD3 exomes AF: 0.104 AC: 26141AN: 251458Hom.: 1810 AF XY: 0.109 AC XY: 14753AN XY: 135900
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GnomAD4 exome AF: 0.114 AC: 166038AN: 1459748Hom.: 10585 Cov.: 31 AF XY: 0.115 AC XY: 83202AN XY: 726274
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GnomAD4 genome ? AF: 0.0900 AC: 13706AN: 152250Hom.: 866 Cov.: 32 AF XY: 0.0906 AC XY: 6748AN XY: 74444
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at