rs7522061

Variant names:

• chr1-157698600-T-A
• rs7522061
• NM_052939.4:c.82A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-157698600-T-A
• chr1-157698600-T-C
• chr1-157698600-T-G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000368184.8(FCRL3):​c.82A>T​(p.Asn28Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FCRL3 ENST00000368184.8 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572
• Publications: 90 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08317137).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000368184.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRL3	NM_052939.4	MANE Select	c.82A>T	p.Asn28Tyr	missense	Exon 4 of 15	NP_443171.2
	FCRL3	NM_001320333.2		c.82A>T	p.Asn28Tyr	missense	Exon 4 of 16	NP_001307262.1
	FCRL3	NR_135214.2		n.286A>T		non_coding_transcript_exon	Exon 4 of 16

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRL3	ENST00000368184.8	TSL:1 MANE Select	c.82A>T	p.Asn28Tyr	missense	Exon 4 of 15	ENSP00000357167.3
	FCRL3	ENST00000368186.9	TSL:1	c.82A>T	p.Asn28Tyr	missense	Exon 4 of 16	ENSP00000357169.5
	FCRL3	ENST00000477837.5	TSL:1	n.82A>T		non_coding_transcript_exon	Exon 4 of 15	ENSP00000433430.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 41

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.094
BayesDel_addAF	Benign	-0.34	T
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.82
DANN	Benign	0.78
DEOGEN2	Benign	0.0045	T
Eigen	Benign	-1.8
Eigen_PC	Benign	-2.0
FATHMM_MKL	Benign	0.024	N
LIST_S2	Benign	0.20	T
M_CAP	Benign	0.0022	T
MetaRNN	Benign	0.083	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.3	L
PhyloP100		-0.57
PrimateAI	Benign	0.25	T
PROVEAN	Benign	-0.84	N
REVEL	Benign	0.048
Sift	Benign	0.034	D
Sift4G	Benign	0.086	T
Polyphen		0.0030	B
Vest4		0.15
MutPred		0.42		Gain of sheet (P = 0.1539)
MVP		0.076
MPC		0.014
ClinPred		0.19	T
GERP RS		-11
Varity_R		0.033
gMVP		0.16
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs7522061; hg19: chr1-157668390;