rs17412751

Variant names:

• chr1-161588331-C-T
• rs17412751
• ENST00000466542.6:c.113-91C>T

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 2 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: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000466542.6. 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
	FCGR2C	NR_047648.1		n.212-91C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCGR2C	ENST00000466542.6	TSL:1	c.113-91C>T		intron	N/A	ENSP00000426627.1
	ENSG00000289768	ENST00000699402.1		c.41-39300G>A		intron	N/A	ENSP00000514363.1	A0A8V8TN80
	FCGR2C	ENST00000465075.6	TSL:1	n.205-91C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0217 AC: 7 AN: 322 Hom.: 0 Cov.: 0

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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 34

American (AMR) AF: 0.0179 AC: 45 AN: 2512

Ashkenazi Jewish (ASJ) AF: 0.00926 AC: 1 AN: 108

East Asian (EAS) AF: 0.00 AC: 0 AN: 524

South Asian (SAS) AF: 0.0144 AC: 35 AN: 2424

European-Finnish (FIN) AF: 0.00538 AC: 1 AN: 186

Middle Eastern (MID) AF: 0.0625 AC: 1 AN: 16

European-Non Finnish (NFE) AF: 0.0228 AC: 162 AN: 7092

Other (OTH) AF: 0.0268 AC: 14 AN: 522

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 50

American (AMR) AF: 0.00 AC: 0 AN: 36

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 2 AN: 14

East Asian (EAS) AF: 0.00 AC: 0 AN: 32

South Asian (SAS) AF: 0.0385 AC: 1 AN: 26

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0253 AC: 4 AN: 158

Other (OTH) AF: 0.00 AC: 0 AN: 2

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.00801702), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0578 Hom.: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.89
DANN	Benign	0.61
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17412751;

hg19: chr1-161558121;