rs4656308

chr1-161508961-C-T

Variant summary

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

The NM_001136219.3(FCGR2A):c.365-859C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,192 control chromosomes in the GnomAD database, including 52,867 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 0.83 (52867 hom., cov: 33)
• Consequence: FCGR2A NM_001136219.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCGR2A	NM_001136219.3	c.365-859C>T		intron_variant		ENST00000271450.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCGR2A	ENST00000271450.12	c.365-859C>T		intron_variant		1	NM_001136219.3	A2

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125961 AN: 152074 Hom.: 52816 Cov.: 33

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.822

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.828 AC: 126068 AN: 152192 Hom.: 52867 Cov.: 33 AF XY: 0.826 AC XY: 61401 AN XY: 74380

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.820

Alfa AF: 0.791 Hom.: 8126

Bravo AF: 0.841

Asia WGS AF: 0.779 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.90
Dann	Benign	0.23

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: rs4656308; hg19: chr1-161478751;