dbSNP rs6427598: FCGR2A:c.780+842T>A (chr1-161514774-T-A) – ACMG Classification: Uncertain_significance (0 pts)

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.530

Publications

4 publications found

Variant links:

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]

FCGR2A links:

ENSG00000273112 (HGNC:):

ENSG00000273112 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001136219.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136219.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FCGR2A	NM_001136219.3	MANE Select	c.780+842T>A	intron	N/A	NP_001129691.1	P12318-1
FCGR2A	NM_021642.5		c.777+842T>A	intron	N/A	NP_067674.2	P12318-2
FCGR2A	NM_001375296.1		c.657+842T>A	intron	N/A	NP_001362225.1	A0A8V8TPS4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FCGR2A	ENST00000271450.12	TSL:1 MANE Select	c.780+842T>A	intron	N/A	ENSP00000271450.6	P12318-1
FCGR2A	ENST00000367972.8	TSL:1	c.777+842T>A	intron	N/A	ENSP00000356949.4	P12318-2
FCGR2A	ENST00000967690.1		c.837+842T>A	intron	N/A	ENSP00000637749.1

Frequencies

GnomAD3 genomes

AF:

0.527

AC:

73472

AN:

139290

Hom.:

13424

Cov.:

show subpopulations

Gnomad AFR

AF:

0.641

Gnomad AMI

AF:

0.418

Gnomad AMR

AF:

0.500

Gnomad ASJ

AF:

0.487

Gnomad EAS

AF:

0.384

Gnomad SAS

AF:

0.484

Gnomad FIN

AF:

0.490

Gnomad MID

AF:

0.482

Gnomad NFE

AF:

0.492

Gnomad OTH

AF:

0.521

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.528

AC:

73543

AN:

139398

Hom.:

13444

Cov.:

AF XY:

0.526

AC XY:

35708

AN XY:

67936

show subpopulations

African (AFR)

AF:

0.641

AC:

23365

AN:

36460

American (AMR)

AF:

0.501

AC:

6995

AN:

13970

Ashkenazi Jewish (ASJ)

AF:

0.487

AC:

1586

AN:

3256

East Asian (EAS)

AF:

0.384

AC:

1814

AN:

4730

South Asian (SAS)

AF:

0.484

AC:

2086

AN:

4308

European-Finnish (FIN)

AF:

0.490

AC:

4786

AN:

9768

Middle Eastern (MID)

AF:

0.477

AC:

124

AN:

260

European-Non Finnish (NFE)

AF:

0.492

AC:

31417

AN:

63852

Other (OTH)

AF:

0.522

AC:

1013

AN:

1940

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.538

Heterozygous variant carriers

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

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:

0.542

Hom.:

1769

Asia WGS

AF:

0.447

AC:

1553

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

0.53

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.21

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.21

Position offset: -44

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over