rs7552317

Positions:

• chr1-161509648-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.365-172C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0995 in 152,272 control chromosomes in the GnomAD database, including 926 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 0.099 (926 hom., cov: 32)
• Consequence: FCGR2A NM_001136219.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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 (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCGR2A	NM_001136219.3	c.365-172C>T		intron_variant		ENST00000271450.12	NP_001129691.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCGR2A	ENST00000271450.12	c.365-172C>T		intron_variant		1	NM_001136219.3	ENSP00000271450	A2

Frequencies

GnomAD3 genomes AF: 0.0996 AC: 15150 AN: 152154 Hom.: 924 Cov.: 32

Gnomad AFR AF: 0.0577

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0859

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0995 AC: 15151 AN: 152272 Hom.: 926 Cov.: 32 AF XY: 0.100 AC XY: 7447 AN XY: 74448

Gnomad4 AFR AF: 0.0578

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0857

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.109

Alfa AF: 0.109 Hom.: 260

Bravo AF: 0.100

Asia WGS AF: 0.0350 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.40
DANN	Benign	0.44

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: rs7552317; hg19: chr1-161479438;