rs1984492

Variant names:

• chr1-157548242-A-G
• rs1984492
• NM_031281.3:c.53-1045T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FCRL5	NM_031281.3	c.53-1045T>C		intron_variant	Intron 2 of 16	ENST00000361835.8	NP_112571.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCRL5	ENST00000361835.8	c.53-1045T>C		intron_variant	Intron 2 of 16	1	NM_031281.3	ENSP00000354691.3
FCRL5	ENST00000368190.7	c.53-1045T>C		intron_variant	Intron 2 of 9	1		ENSP00000357173.3
FCRL5	ENST00000368189.3	c.53-1045T>C		intron_variant	Intron 2 of 7	1		ENSP00000357172.3
FCRL5	ENST00000481082.1	n.158-1045T>C		intron_variant	Intron 2 of 6	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

African (AFR) AF: 0.362 AC: 15037 AN: 41502

American (AMR) AF: 0.193 AC: 2959 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3468

East Asian (EAS) AF: 0.0832 AC: 431 AN: 5180

South Asian (SAS) AF: 0.163 AC: 786 AN: 4828

European-Finnish (FIN) AF: 0.209 AC: 2216 AN: 10614

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14293 AN: 67998

Other (OTH) AF: 0.273 AC: 578 AN: 2114

Alfa AF: 0.216 Hom.: 1474

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
PhyloP100		-0.18
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: rs1984492; hg19: chr1-157518032;