rs6427598

Positions:

• chr1-161514774-T-A
• chr1-161514774-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530

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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCGR2A	NM_001136219.3	c.780+842T>A		intron_variant		ENST00000271450.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCGR2A	ENST00000271450.12	c.780+842T>A		intron_variant		1	NM_001136219.3	A2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 73472 AN: 139290 Hom.: 13424 Cov.: 30 FAILED QC

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: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.528 AC: 73543 AN: 139398 Hom.: 13444 Cov.: 30 AF XY: 0.526 AC XY: 35708 AN XY: 67936

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.522

Alfa AF: 0.542 Hom.: 1769

Asia WGS AF: 0.447 AC: 1553 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	17
DANN	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs6427598; hg19: chr1-161484564; COSMIC: COSV54840440; COSMIC: COSV54840440;