rs11264794

chr1-157677999-C-Achr1-157677999-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052939.4(FCRL3):c.*711G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 984,300 control chromosomes in the GnomAD database, including 159,197 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 0.62 (31220 hom., cov: 31)
  • Exomes 𝑓: 0.55 (127977 hom.)
• Consequence: FCRL3 NM_052939.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

Genes affected

FCRL3 (HGNC:18506): (Fc receptor like 3) This gene encodes a member of the immunoglobulin receptor superfamily and is one of several Fc receptor-like glycoproteins clustered on the long arm of chromosome 1. The encoded protein contains immunoreceptor-tyrosine activation motifs and immunoreceptor-tyrosine inhibitory motifs in its cytoplasmic domain and may play a role in regulation of the immune system. Mutations in this gene have been associated with rheumatoid arthritis, autoimmune thyroid disease, and systemic lupus erythematosus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCRL3	NM_052939.4	c.*711G>T		3_prime_UTR_variant	15/15	ENST00000368184.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCRL3	ENST00000368184.8	c.*711G>T		3_prime_UTR_variant	15/15	1	NM_052939.4	P2

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94134 AN: 151858 Hom.: 31169 Cov.: 31

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.611

GnomAD4 exome AF: 0.552 AC: 459456 AN: 832324 Hom.: 127977 Cov.: 31 AF XY: 0.551 AC XY: 211841 AN XY: 384390

Gnomad4 AFR exome AF: 0.910

Gnomad4 AMR exome AF: 0.459

Gnomad4 ASJ exome AF: 0.558

Gnomad4 EAS exome AF: 0.473

Gnomad4 SAS exome AF: 0.497

Gnomad4 FIN exome AF: 0.471

Gnomad4 NFE exome AF: 0.546

Gnomad4 OTH exome AF: 0.565

GnomAD4 genome AF: 0.620 AC: 94230 AN: 151976 Hom.: 31220 Cov.: 31 AF XY: 0.613 AC XY: 45511 AN XY: 74246

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.614

Alfa AF: 0.555 Hom.: 24717

Bravo AF: 0.638

Asia WGS AF: 0.504 AC: 1750 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.23
Dann	Benign	0.43

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: rs11264794; hg19: chr1-157647789;