rs3845586

Variant names:

• chr1-157514663-G-A
• rs3845586
• NM_031281.3:c.*1012C>T

Variant summary

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

The NM_031281.3(FCRL5):​c.*1012C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 152,160 control chromosomes in the GnomAD database, including 23,860 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 0.52 (23829 hom., cov: 32)
  • Exomes 𝑓: 0.70 (31 hom.)
• Consequence: FCRL5 NM_031281.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCRL5	NM_031281.3	c.*1012C>T		3_prime_UTR_variant	Exon 17 of 17	ENST00000361835.8	NP_112571.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCRL5	ENST00000361835	c.*1012C>T		3_prime_UTR_variant	Exon 17 of 17	1	NM_031281.3	ENSP00000354691.3
FCRL5	ENST00000461387.5	n.3223C>T		non_coding_transcript_exon_variant	Exon 7 of 7	2
FCRL5	ENST00000462218.1	n.1334C>T		non_coding_transcript_exon_variant	Exon 2 of 2	2
FCRL5	ENST00000497286.5	n.3039C>T		non_coding_transcript_exon_variant	Exon 9 of 9	2

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78533 AN: 151918 Hom.: 23826 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.541

GnomAD4 exome AF: 0.697 AC: 85 AN: 122 Hom.: 31 Cov.: 0 AF XY: 0.714 AC XY: 70 AN XY: 98

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.750

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.704

GnomAD4 genome AF: 0.517 AC: 78538 AN: 152038 Hom.: 23829 Cov.: 32 AF XY: 0.529 AC XY: 39292 AN XY: 74320

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.537

Alfa AF: 0.607 Hom.: 29038

Bravo AF: 0.498

Asia WGS AF: 0.683 AC: 2373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.95
DANN	Benign	0.25

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: rs3845586; hg19: chr1-157484453;