rs3811036

Positions:

• chr1-157515485-T-G

Variant summary

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

The NM_031281.3(FCRL5):​c.*190A>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 0.0968 in 1,272,072 control chromosomes in the GnomAD database, including 10,658 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 0.18 (4280 hom., cov: 33)
  • Exomes 𝑓: 0.086 (6378 hom.)
• Consequence: FCRL5 NM_031281.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCRL5	NM_031281.3	c.*190A>C		3_prime_UTR_variant	17/17	ENST00000361835.8	NP_112571.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCRL5	ENST00000361835.8	c.*190A>C		3_prime_UTR_variant	17/17	1	NM_031281.3	ENSP00000354691	P1
FCRL5	ENST00000461387.5	n.2401A>C		non_coding_transcript_exon_variant	7/7	2
FCRL5	ENST00000462218.1	n.512A>C		non_coding_transcript_exon_variant	2/2	2
FCRL5	ENST00000497286.5	n.2217A>C		non_coding_transcript_exon_variant	9/9	2

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27011 AN: 152090 Hom.: 4278 Cov.: 33

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.161

GnomAD4 exome AF: 0.0858 AC: 96122 AN: 1119864 Hom.: 6378 Cov.: 15 AF XY: 0.0863 AC XY: 48192 AN XY: 558424

Gnomad4 AFR exome AF: 0.453

Gnomad4 AMR exome AF: 0.0764

Gnomad4 ASJ exome AF: 0.0731

Gnomad4 EAS exome AF: 0.101

Gnomad4 SAS exome AF: 0.128

Gnomad4 FIN exome AF: 0.0533

Gnomad4 NFE exome AF: 0.0714

Gnomad4 OTH exome AF: 0.106

GnomAD4 genome AF: 0.178 AC: 27047 AN: 152208 Hom.: 4280 Cov.: 33 AF XY: 0.174 AC XY: 12945 AN XY: 74412

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0712

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0570

Gnomad4 NFE AF: 0.0746

Gnomad4 OTH AF: 0.162

Alfa AF: 0.0974 Hom.: 750

Bravo AF: 0.193

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.61

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: rs3811036; hg19: chr1-157485275; COSMIC: COSV62513430; COSMIC: COSV62513430;