1-161589537-A-G

Variant names:

• chr1-161589537-A-G
• rs3933769
• ENST00000466542.6:c.134-25A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000466542.6(FCGR2C):​c.134-25A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 1,550,036 control chromosomes in the GnomAD database, including 458,326 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 0.70 (38077 hom., cov: 26)
  • Exomes 𝑓: 0.74 (420249 hom.)
• Consequence: FCGR2C ENST00000466542.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 17 publications found

Genes affected

FCGR2C (HGNC:15626): (Fc gamma receptor IIc (gene/pseudogene)) This gene encodes one of three members of a family of low-affinity immunoglobulin gamma Fc receptors found on the surface of many immune response cells. The encoded protein is a transmembrane glycoprotein and may be involved in phagocytosis and clearing of immune complexes. An allelic polymorphism in this gene results in both coding and non-coding variants. [provided by RefSeq, Apr 2012]

ENSG00000289768 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCGR2C	NR_047648.1	n.233-25A>G		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCGR2C	ENST00000466542.6	c.134-25A>G		intron_variant	Intron 2 of 6	1		ENSP00000426627.1
ENSG00000289768	ENST00000699402.1	c.41-40506T>C		intron_variant	Intron 1 of 3			ENSP00000514363.1

Frequencies

GnomAD3 genomes AF: 0.702 AC: 98859 AN: 140840 Hom.: 38041 Cov.: 26

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.705

GnomAD2 exomes AF: 0.741 AC: 177272 AN: 239272 AF XY: 0.738

Gnomad AFR exome AF: 0.596

Gnomad AMR exome AF: 0.855

Gnomad ASJ exome AF: 0.604

Gnomad EAS exome AF: 0.752

Gnomad FIN exome AF: 0.802

Gnomad NFE exome AF: 0.729

Gnomad OTH exome AF: 0.728

GnomAD4 exome AF: 0.742 AC: 1046062 AN: 1409074 Hom.: 420249 Cov.: 65 AF XY: 0.740 AC XY: 518557 AN XY: 700402

African (AFR) AF: 0.602 AC: 19547 AN: 32484

American (AMR) AF: 0.843 AC: 36913 AN: 43790

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 15021 AN: 24594

East Asian (EAS) AF: 0.811 AC: 32094 AN: 39574

South Asian (SAS) AF: 0.725 AC: 60908 AN: 84020

European-Finnish (FIN) AF: 0.805 AC: 41296 AN: 51290

Middle Eastern (MID) AF: 0.630 AC: 3378 AN: 5366

European-Non Finnish (NFE) AF: 0.743 AC: 794995 AN: 1069740

Other (OTH) AF: 0.720 AC: 41910 AN: 58216

GnomAD4 genome AF: 0.702 AC: 98945 AN: 140962 Hom.: 38077 Cov.: 26 AF XY: 0.705 AC XY: 48306 AN XY: 68494

African (AFR) AF: 0.596 AC: 22739 AN: 38140

American (AMR) AF: 0.772 AC: 10804 AN: 13992

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 1948 AN: 3196

East Asian (EAS) AF: 0.762 AC: 3854 AN: 5060

South Asian (SAS) AF: 0.733 AC: 3256 AN: 4440

European-Finnish (FIN) AF: 0.806 AC: 7626 AN: 9458

Middle Eastern (MID) AF: 0.604 AC: 168 AN: 278

European-Non Finnish (NFE) AF: 0.733 AC: 46651 AN: 63604

Other (OTH) AF: 0.709 AC: 1345 AN: 1898

Alfa AF: 0.709 Hom.: 8125

Asia WGS AF: 0.755 AC: 2580 AN: 3418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.57
DANN	Benign	0.36
PhyloP100		-2.2
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: rs3933769; hg19: chr1-161559327;