rs17416676

chr1-157534015-G-Achr1-157534015-G-T

Variant summary

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

The ENST00000368189.3(FCRL5):c.*501C>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 0.217 in 178,768 control chromosomes in the GnomAD database, including 5,154 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 0.21 (4281 hom., cov: 32)
  • Exomes 𝑓: 0.25 (873 hom.)
• Consequence: FCRL5 ENST00000368189.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCRL5	NM_031281.3	c.1681+599C>T		intron_variant		ENST00000361835.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCRL5	ENST00000368189.3	c.*501C>T		3_prime_UTR_variant	8/8	1
FCRL5	ENST00000361835.8	c.1681+599C>T		intron_variant		1	NM_031281.3	P1
FCRL5	ENST00000368190.7	c.1681+599C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32230 AN: 151948 Hom.: 4279 Cov.: 32

Gnomad AFR AF: 0.0526

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.232

GnomAD4 exome AF: 0.249 AC: 6644 AN: 26702 Hom.: 873 Cov.: 0 AF XY: 0.243 AC XY: 3403 AN XY: 13996

Gnomad4 AFR exome AF: 0.0460

Gnomad4 AMR exome AF: 0.220

Gnomad4 ASJ exome AF: 0.372

Gnomad4 EAS exome AF: 0.0928

Gnomad4 SAS exome AF: 0.276

Gnomad4 FIN exome AF: 0.249

Gnomad4 NFE exome AF: 0.265

Gnomad4 OTH exome AF: 0.262

GnomAD4 genome AF: 0.212 AC: 32235 AN: 152066 Hom.: 4281 Cov.: 32 AF XY: 0.212 AC XY: 15794 AN XY: 74350

Gnomad4 AFR AF: 0.0524

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.233

Alfa AF: 0.267 Hom.: 5168

Bravo AF: 0.204

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	5.6
Dann	Benign	0.50

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: rs17416676; hg19: chr1-157503805;