1-161724664-A-G

Position:

• chr1-161724664-A-G

Variant summary

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

The NM_001002901.4(FCRLB):​c.307+1043A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,022 control chromosomes in the GnomAD database, including 27,449 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 0.59 (27449 hom., cov: 32)
• Consequence: FCRLB NM_001002901.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCRLB	NM_001002901.4	c.307+1043A>G		intron_variant		ENST00000367948.7	NP_001002901.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCRLB	ENST00000367948.7	c.307+1043A>G		intron_variant		1	NM_001002901.4	ENSP00000356925.2

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89022 AN: 151904 Hom.: 27431 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.586 AC: 89065 AN: 152022 Hom.: 27449 Cov.: 32 AF XY: 0.585 AC XY: 43482 AN XY: 74290

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.658

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.625

Alfa AF: 0.621 Hom.: 13416

Bravo AF: 0.570

Asia WGS AF: 0.643 AC: 2234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.5
DANN	Benign	0.69

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: rs1891020; hg19: chr1-161694454;