chr1-161514774-T-A

Variant names:

• chr1-161514774-T-A
• rs6427598
• NM_001136219.3:c.780+842T>A

Variant summary

Our verdict is Uncertain significance. The variant received 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
• Publications: 4 publications found

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]

ENSG00000273112 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCGR2A	NM_001136219.3	c.780+842T>A		intron_variant	Intron 6 of 6	ENST00000271450.12	NP_001129691.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCGR2A	ENST00000271450.12	c.780+842T>A		intron_variant	Intron 6 of 6	1	NM_001136219.3	ENSP00000271450.6

Frequencies

GnomAD3 genomes AF: 0.527 AC: 73472 AN: 139290 Hom.: 13424 Cov.: 30

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.641 AC: 23365 AN: 36460

American (AMR) AF: 0.501 AC: 6995 AN: 13970

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1586 AN: 3256

East Asian (EAS) AF: 0.384 AC: 1814 AN: 4730

South Asian (SAS) AF: 0.484 AC: 2086 AN: 4308

European-Finnish (FIN) AF: 0.490 AC: 4786 AN: 9768

Middle Eastern (MID) AF: 0.477 AC: 124 AN: 260

European-Non Finnish (NFE) AF: 0.492 AC: 31417 AN: 63852

Other (OTH) AF: 0.522 AC: 1013 AN: 1940

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
PhyloP100		0.53
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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