rs368433

chr1-161514420-T-C

Variant summary

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

The NM_001136219.3(FCGR2A):c.780+488T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0785 in 139,040 control chromosomes in the GnomAD database, including 630 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 0.078 (630 hom., cov: 30)
• Consequence: FCGR2A NM_001136219.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCGR2A	NM_001136219.3	c.780+488T>C		intron_variant		ENST00000271450.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCGR2A	ENST00000271450.12	c.780+488T>C		intron_variant		1	NM_001136219.3	A2

Frequencies

GnomAD3 genomes AF: 0.0785 AC: 10903 AN: 138942 Hom.: 628 Cov.: 30

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.0802

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.0479

Gnomad FIN AF: 0.0863

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.0988

Gnomad OTH AF: 0.0818

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

GnomAD4 genome AF: 0.0785 AC: 10908 AN: 139040 Hom.: 630 Cov.: 30 AF XY: 0.0777 AC XY: 5260 AN XY: 67686

Gnomad4 AFR AF: 0.0452

Gnomad4 AMR AF: 0.0800

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.0165

Gnomad4 SAS AF: 0.0477

Gnomad4 FIN AF: 0.0863

Gnomad4 NFE AF: 0.0988

Gnomad4 OTH AF: 0.0813

Alfa AF: 0.101 Hom.: 116

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.84
Dann	Benign	0.73

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: rs368433; hg19: chr1-161484210; COSMIC: COSV54839528; COSMIC: COSV54839528;