rs3843307

chr1-157514785-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.*890T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,148 control chromosomes in the GnomAD database, including 30,210 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 0.61 (30200 hom., cov: 33)
  • Exomes 𝑓: 0.68 (10 hom.)
• Consequence: FCRL5 NM_031281.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.630

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCRL5	NM_031281.3	c.*890T>C		3_prime_UTR_variant	17/17	ENST00000361835.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCRL5	ENST00000361835.8	c.*890T>C		3_prime_UTR_variant	17/17	1	NM_031281.3	P1
FCRL5	ENST00000461387.5	n.3101T>C		non_coding_transcript_exon_variant	7/7	2
FCRL5	ENST00000462218.1	n.1212T>C		non_coding_transcript_exon_variant	2/2	2
FCRL5	ENST00000497286.5	n.2917T>C		non_coding_transcript_exon_variant	9/9	2

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93449 AN: 151986 Hom.: 30192 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.621

GnomAD4 exome AF: 0.682 AC: 30 AN: 44 Hom.: 10 Cov.: 0 AF XY: 0.658 AC XY: 25 AN XY: 38

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.700

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.615 AC: 93483 AN: 152104 Hom.: 30200 Cov.: 33 AF XY: 0.622 AC XY: 46240 AN XY: 74354

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.616

Alfa AF: 0.673 Hom.: 73956

Bravo AF: 0.602

Asia WGS AF: 0.708 AC: 2461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.7
Dann	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3843307; hg19: chr1-157484575;