rs11264794

Variant names:

• chr1-157677999-C-A
• rs11264794
• NM_052939.4:c.*711G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-157677999-C-A
• chr1-157677999-C-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FCRL3	NM_052939.4	c.*711G>T		3_prime_UTR_variant	Exon 15 of 15	ENST00000368184.8	NP_443171.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCRL3	ENST00000368184.8	c.*711G>T		3_prime_UTR_variant	Exon 15 of 15	1	NM_052939.4	ENSP00000357167.3

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

African (AFR) AF: 0.910 AC: 14351 AN: 15776

American (AMR) AF: 0.459 AC: 451 AN: 982

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 2869 AN: 5142

East Asian (EAS) AF: 0.473 AC: 1715 AN: 3624

South Asian (SAS) AF: 0.497 AC: 8167 AN: 16442

European-Finnish (FIN) AF: 0.471 AC: 130 AN: 276

Middle Eastern (MID) AF: 0.599 AC: 970 AN: 1620

European-Non Finnish (NFE) AF: 0.546 AC: 415376 AN: 761180

Other (OTH) AF: 0.565 AC: 15427 AN: 27282

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

African (AFR) AF: 0.878 AC: 36462 AN: 41508

American (AMR) AF: 0.529 AC: 8074 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1982 AN: 3462

East Asian (EAS) AF: 0.479 AC: 2473 AN: 5160

South Asian (SAS) AF: 0.468 AC: 2254 AN: 4820

European-Finnish (FIN) AF: 0.475 AC: 4995 AN: 10514

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36052 AN: 67946

Other (OTH) AF: 0.614 AC: 1292 AN: 2104

Alfa AF: 0.567 Hom.: 33693

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
PhyloP100		-2.0
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: rs11264794; hg19: chr1-157647789;