1-161724664-A-G

Variant names:

• chr1-161724664-A-G
• rs1891020
• NM_001002901.4:c.307+1043A>G

Variant summary

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001002901.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRLB	NM_001002901.4	MANE Select	c.307+1043A>G		intron	N/A	NP_001002901.1
	FCRLB	NM_001320241.1		c.307+1043A>G		intron	N/A	NP_001307170.1
	FCRLB	NM_001288829.1		c.307+1043A>G		intron	N/A	NP_001275758.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRLB	ENST00000367948.7	TSL:1 MANE Select	c.307+1043A>G		intron	N/A	ENSP00000356925.2
	FCRLB	ENST00000367946.7	TSL:1	c.307+1043A>G		intron	N/A	ENSP00000356923.3
	FCRLB	ENST00000367945.5	TSL:1	c.286+1043A>G		intron	N/A	ENSP00000356922.1

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

African (AFR) AF: 0.397 AC: 16427 AN: 41424

American (AMR) AF: 0.547 AC: 8351 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2284 AN: 3470

East Asian (EAS) AF: 0.808 AC: 4188 AN: 5184

South Asian (SAS) AF: 0.548 AC: 2645 AN: 4824

European-Finnish (FIN) AF: 0.681 AC: 7191 AN: 10552

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46043 AN: 67982

Other (OTH) AF: 0.625 AC: 1319 AN: 2112

Alfa AF: 0.623 Hom.: 15221

Bravo AF: 0.570

Asia WGS AF: 0.643 AC: 2234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.5
DANN	Benign	0.69
PhyloP100		0.27
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: rs1891020; hg19: chr1-161694454;