rs1984492

chr1-157548242-A-G

Variant summary

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

The NM_031281.3(FCRL5):c.53-1045T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,204 control chromosomes in the GnomAD database, including 5,038 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 0.25 (5038 hom., cov: 33)
• Consequence: FCRL5 NM_031281.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

Genes affected

FCRL5 (HGNC:18508): (Fc receptor like 5) This gene encodes a member of the immunoglobulin receptor superfamily and the Fc-receptor like family. This gene and several other Fc receptor-like gene members are clustered on the long arm of chromosome 1. The encoded protein is a single-pass type I membrane protein and contains 8 immunoglobulin-like C2-type domains. This gene is implicated in B cell development and lymphomagenesis. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Sep 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCRL5	NM_031281.3	c.53-1045T>C		intron_variant		ENST00000361835.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCRL5	ENST00000361835.8	c.53-1045T>C		intron_variant		1	NM_031281.3	P1
FCRL5	ENST00000368189.3	c.53-1045T>C		intron_variant		1
FCRL5	ENST00000368190.7	c.53-1045T>C		intron_variant		1
FCRL5	ENST00000481082.1	n.158-1045T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37436 AN: 152086 Hom.: 5036 Cov.: 33

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.0834

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.246 AC: 37468 AN: 152204 Hom.: 5038 Cov.: 33 AF XY: 0.241 AC XY: 17951 AN XY: 74438

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.0832

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.273

Alfa AF: 0.216 Hom.: 1339

Bravo AF: 0.249

Asia WGS AF: 0.166 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.4
Dann	Benign	0.58

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: rs1984492; hg19: chr1-157518032;