rs3900770

Positions:

• chr1-157514908-T-C

Variant summary

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

The NM_031281.3(FCRL5):​c.*767A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0952 in 152,360 control chromosomes in the GnomAD database, including 1,241 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 0.095 (1241 hom., cov: 33)
  • Exomes 𝑓: 0.068 (0 hom.)
• Consequence: FCRL5 NM_031281.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCRL5	NM_031281.3	c.*767A>G		3_prime_UTR_variant	17/17	ENST00000361835.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCRL5	ENST00000361835.8	c.*767A>G		3_prime_UTR_variant	17/17	1	NM_031281.3	P1
FCRL5	ENST00000461387.5	n.2978A>G		non_coding_transcript_exon_variant	7/7	2
FCRL5	ENST00000462218.1	n.1089A>G		non_coding_transcript_exon_variant	2/2	2
FCRL5	ENST00000497286.5	n.2794A>G		non_coding_transcript_exon_variant	9/9	2

Frequencies

GnomAD3 genomes AF: 0.0952 AC: 14486 AN: 152110 Hom.: 1239 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0600

Gnomad ASJ AF: 0.0504

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0750

GnomAD4 exome AF: 0.0682 AC: 9 AN: 132 Hom.: 0 Cov.: 0 AF XY: 0.0897 AC XY: 7 AN XY: 78

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0702

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0952 AC: 14495 AN: 152228 Hom.: 1241 Cov.: 33 AF XY: 0.0906 AC XY: 6743 AN XY: 74440

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.0599

Gnomad4 ASJ AF: 0.0504

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0164

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0515

Gnomad4 OTH AF: 0.0743

Alfa AF: 0.0588 Hom.: 482

Bravo AF: 0.102

Asia WGS AF: 0.0230 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.57

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: rs3900770; hg19: chr1-157484698;