rs17412751

Positions:

• chr1-161588331-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000466542.6(FCGR2C):​c.113-91C>T 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 0.022 (0 hom., cov: 0)
  • Exomes 𝑓: 0.019 (2 hom.)
  • Failed GnomAD Quality Control
• Consequence: FCGR2C ENST00000466542.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCGR2C	NR_047648.1	n.212-91C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCGR2C	ENST00000466542.6	c.113-91C>T		intron_variant		1		ENSP00000426627	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 7 AN: 322 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0417

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0253

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0193 AC: 259 AN: 13418 Hom.: 2 Cov.: 0 AF XY: 0.0190 AC XY: 138 AN XY: 7278

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0179

Gnomad4 ASJ exome AF: 0.00926

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0144

Gnomad4 FIN exome AF: 0.00538

Gnomad4 NFE exome AF: 0.0228

Gnomad4 OTH exome AF: 0.0268

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0216 AC: 7 AN: 324 Hom.: 0 Cov.: 0 AF XY: 0.0145 AC XY: 2 AN XY: 138

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0385

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0253

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0578 Hom.: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.89
DANN	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs17412751; hg19: chr1-161558121;