rs13878

Positions:

• chr1-161518174-T-C
• chr1-161518174-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001136219.3(FCGR2A):​c.*26T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00821 in 1,573,036 control chromosomes in the GnomAD database, including 1,082 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 0.014 (112 hom., cov: 33)
  • Exomes 𝑓: 0.0076 (970 hom.)
• Consequence: FCGR2A NM_001136219.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCGR2A	NM_001136219.3	c.*26T>C		3_prime_UTR_variant	7/7	ENST00000271450.12	NP_001129691.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCGR2A	ENST00000271450.12	c.*26T>C		3_prime_UTR_variant	7/7	1	NM_001136219.3	ENSP00000271450	A2

Frequencies

GnomAD3 genomes AF: 0.0145 AC: 2039 AN: 140728 Hom.: 111 Cov.: 33

Gnomad AFR AF: 0.00943

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0195

Gnomad ASJ AF: 0.00649

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.0619

Gnomad FIN AF: 0.00276

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000952

Gnomad OTH AF: 0.0133

GnomAD3 exomes AF: 0.0141 AC: 3379 AN: 239142 Hom.: 298 AF XY: 0.0139 AC XY: 1794 AN XY: 129192

Gnomad AFR exome AF: 0.00356

Gnomad AMR exome AF: 0.0123

Gnomad ASJ exome AF: 0.00187

Gnomad EAS exome AF: 0.142

Gnomad SAS exome AF: 0.0222

Gnomad FIN exome AF: 0.00121

Gnomad NFE exome AF: 0.000180

Gnomad OTH exome AF: 0.00867

GnomAD4 exome AF: 0.00760 AC: 10878 AN: 1432184 Hom.: 970 Cov.: 31 AF XY: 0.00856 AC XY: 6091 AN XY: 711274

Gnomad4 AFR exome AF: 0.00326

Gnomad4 AMR exome AF: 0.0123

Gnomad4 ASJ exome AF: 0.00295

Gnomad4 EAS exome AF: 0.191

Gnomad4 SAS exome AF: 0.0295

Gnomad4 FIN exome AF: 0.00122

Gnomad4 NFE exome AF: 0.000183

Gnomad4 OTH exome AF: 0.00595

GnomAD4 genome AF: 0.0145 AC: 2036 AN: 140852 Hom.: 112 Cov.: 33 AF XY: 0.0168 AC XY: 1155 AN XY: 68774

Gnomad4 AFR AF: 0.00938

Gnomad4 AMR AF: 0.0195

Gnomad4 ASJ AF: 0.00649

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.0621

Gnomad4 FIN AF: 0.00276

Gnomad4 NFE AF: 0.000952

Gnomad4 OTH AF: 0.0137

Alfa AF: 0.00675 Hom.: 7

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.6
DANN	Benign	0.83
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs13878; hg19: chr1-161487964;