NM_001002901.4:c.308-754G>A

Variant names:

• chr1-161725067-G-A
• rs12079477
• NM_001002901.4:c.308-754G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001002901.4(FCRLB):​c.308-754G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,150 control chromosomes in the GnomAD database, including 2,351 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 0.15 (2351 hom., cov: 32)
• Consequence: FCRLB NM_001002901.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847
• Publications: 12 publications found

Genes affected

FCRLB (HGNC:26431): (Fc receptor like B) FCRL2 belongs to the Fc receptor family. Fc receptors are involved in phagocytosis, antibody-dependent cell cytotoxicity, immediate hypersensitivity, and transcytosis of immunoglobulins via their ability to bind immunoglobulin (Ig) constant regions (Chikaev et al., 2005 [PubMed 15676285]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCRLB	NM_001002901.4	c.308-754G>A		intron_variant	Intron 5 of 7	ENST00000367948.7	NP_001002901.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCRLB	ENST00000367948.7	c.308-754G>A		intron_variant	Intron 5 of 7	1	NM_001002901.4	ENSP00000356925.2

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23430 AN: 152032 Hom.: 2343 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.0847

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.153

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.154 AC: 23463 AN: 152150 Hom.: 2351 Cov.: 32 AF XY: 0.154 AC XY: 11444 AN XY: 74386

African (AFR) AF: 0.219 AC: 9090 AN: 41472

American (AMR) AF: 0.130 AC: 1987 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0916 AC: 318 AN: 3470

East Asian (EAS) AF: 0.505 AC: 2610 AN: 5164

South Asian (SAS) AF: 0.0837 AC: 404 AN: 4826

European-Finnish (FIN) AF: 0.101 AC: 1075 AN: 10598

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7622 AN: 68004

Other (OTH) AF: 0.151 AC: 318 AN: 2110

Alfa AF: 0.129 Hom.: 6787

Bravo AF: 0.165

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.65
DANN	Benign	0.61
PhyloP100		-0.85
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12079477; hg19: chr1-161694857;