1-161509955-A-T

Variant names:

• chr1-161509955-A-T
• rs1801274
• NM_001136219.3:c.500A>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001136219.3(FCGR2A):​c.500A>T​(p.His167Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H167R) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FCGR2A NM_001136219.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 0 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]

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.0899986).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCGR2A	NM_001136219.3	c.500A>T	p.His167Leu	missense_variant	Exon 4 of 7	ENST00000271450.12	NP_001129691.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCGR2A	ENST00000271450.12	c.500A>T	p.His167Leu	missense_variant	Exon 4 of 7	1	NM_001136219.3	ENSP00000271450.6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 106

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	0.020
DANN	Benign	0.50
DEOGEN2	Benign	0.18	.;T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.0095	N
LIST_S2	Benign	0.22	T;T
M_CAP	Benign	0.0027	T
MetaRNN	Benign	0.090	T;T
MetaSVM	Benign	-0.93	T
MutationAssessor	Uncertain	2.0	.;M
PhyloP100		-0.46
PrimateAI	Benign	0.30	T
PROVEAN	Pathogenic	-5.0	D;D
REVEL	Benign	0.055
Sift	Uncertain	0.0030	D;D
Sift4G	Benign	0.25	T;T
Polyphen		0.023	B;B
Vest4		0.12
MutPred		0.38		.;Loss of disorder (P = 0.0396);
MVP		0.32
MPC		0.28
ClinPred		0.34	T
GERP RS		-4.2
Varity_R		0.64
gMVP		0.71
Mutation Taster		=97/3	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1801274; hg19: chr1-161479745;