chr1-161509648-C-T

Variant names:

• chr1-161509648-C-T
• rs7552317
• NM_001136219.3:c.365-172C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136219.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCGR2A	NM_001136219.3	MANE Select	c.365-172C>T		intron	N/A	NP_001129691.1
	FCGR2A	NM_021642.5		c.362-172C>T		intron	N/A	NP_067674.2
	FCGR2A	NM_001375296.1		c.365-172C>T		intron	N/A	NP_001362225.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCGR2A	ENST00000271450.12	TSL:1 MANE Select	c.365-172C>T		intron	N/A	ENSP00000271450.6
	FCGR2A	ENST00000367972.8	TSL:1	c.362-172C>T		intron	N/A	ENSP00000356949.4
	FCGR2A	ENST00000967690.1		c.365-172C>T		intron	N/A	ENSP00000637749.1

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

African (AFR) AF: 0.0578 AC: 2400 AN: 41550

American (AMR) AF: 0.105 AC: 1599 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 876 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.0857 AC: 414 AN: 4828

European-Finnish (FIN) AF: 0.110 AC: 1165 AN: 10606

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.123 AC: 8350 AN: 68014

Other (OTH) AF: 0.109 AC: 231 AN: 2112

Alfa AF: 0.108 Hom.: 261

Bravo AF: 0.100

Asia WGS AF: 0.0350 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.40
DANN	Benign	0.44
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7552317; hg19: chr1-161479438;