1-157699488-C-T

Position:

• chr1-157699488-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_052939.4(FCRL3):​c.52+204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 149,406 control chromosomes in the GnomAD database, including 18,368 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 0.49 (18368 hom., cov: 26)
• Consequence: FCRL3 NM_052939.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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]

FCRL3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCRL3	NM_052939.4	c.52+204G>A		intron_variant		ENST00000368184.8	NP_443171.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCRL3	ENST00000368184.8	c.52+204G>A		intron_variant		1	NM_052939.4	ENSP00000357167.3

Frequencies

GnomAD3 genomes AF: 0.489 AC: 73083 AN: 149306 Hom.: 18338 Cov.: 26

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.478

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.490 AC: 73150 AN: 149406 Hom.: 18368 Cov.: 26 AF XY: 0.486 AC XY: 35312 AN XY: 72644

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.481

Alfa AF: 0.428 Hom.: 11774

Bravo AF: 0.501

Asia WGS AF: 0.416 AC: 1446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.23		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.23		Position offset: -2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3761959; hg19: chr1-157669278;