chr1-161514774-T-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_001136219.3(FCGR2A):c.780+842T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.53 ( 13444 hom., cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FCGR2A
NM_001136219.3 intron
NM_001136219.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.530
Publications
4 publications found
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.527 AC: 73472AN: 139290Hom.: 13424 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
73472
AN:
139290
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 2Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 2
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
2
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
2
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
0
AN:
2
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.528 AC: 73543AN: 139398Hom.: 13444 Cov.: 30 AF XY: 0.526 AC XY: 35708AN XY: 67936 show subpopulations
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
AC:
73543
AN:
139398
Hom.:
Cov.:
30
AF XY:
AC XY:
35708
AN XY:
67936
show subpopulations
African (AFR)
AF:
AC:
23365
AN:
36460
American (AMR)
AF:
AC:
6995
AN:
13970
Ashkenazi Jewish (ASJ)
AF:
AC:
1586
AN:
3256
East Asian (EAS)
AF:
AC:
1814
AN:
4730
South Asian (SAS)
AF:
AC:
2086
AN:
4308
European-Finnish (FIN)
AF:
AC:
4786
AN:
9768
Middle Eastern (MID)
AF:
AC:
124
AN:
260
European-Non Finnish (NFE)
AF:
AC:
31417
AN:
63852
Other (OTH)
AF:
AC:
1013
AN:
1940
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.538
Heterozygous variant carriers
0
1307
2613
3920
5226
6533
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
722
1444
2166
2888
3610
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
1553
AN:
3474
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -44
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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