rs12079477

chr1-161725067-G-Achr1-161725067-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FCRLB	NM_001002901.4	c.308-754G>A		intron_variant		ENST00000367948.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCRLB	ENST00000367948.7	c.308-754G>A		intron_variant		1	NM_001002901.4	P1

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

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.0916

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.0837

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.151

Alfa AF: 0.121 Hom.: 2639

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

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: rs12079477; hg19: chr1-161694857;