chr1-161726298-T-C

Variant names:

• chr1-161726298-T-C
• rs1417582
• ENST00000495397.1:n.398T>C

Variant summary

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

The ENST00000495397.1(FCRLB):​n.398T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 862,640 control chromosomes in the GnomAD database, including 182,466 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 0.60 (28079 hom., cov: 31)
  • Exomes 𝑓: 0.65 (154387 hom.)
• Consequence: FCRLB ENST00000495397.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 14 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000495397.1. 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.574+211T>C		intron	N/A	NP_001002901.1
	FCRLB	NM_001320241.1		c.574+211T>C		intron	N/A	NP_001307170.1
	FCRLB	NM_001288829.1		c.574+211T>C		intron	N/A	NP_001275758.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRLB	ENST00000495397.1	TSL:1	n.398T>C		non_coding_transcript_exon	Exon 1 of 2
	FCRLB	ENST00000367948.7	TSL:1 MANE Select	c.574+211T>C		intron	N/A	ENSP00000356925.2
	FCRLB	ENST00000367946.7	TSL:1	c.574+211T>C		intron	N/A	ENSP00000356923.3

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90437 AN: 151778 Hom.: 28062 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.632

GnomAD2 exomes AF: 0.618 AC: 84043 AN: 136092 AF XY: 0.618

Gnomad AFR exome AF: 0.409

Gnomad AMR exome AF: 0.485

Gnomad ASJ exome AF: 0.655

Gnomad EAS exome AF: 0.832

Gnomad FIN exome AF: 0.681

Gnomad NFE exome AF: 0.678

Gnomad OTH exome AF: 0.645

GnomAD4 exome AF: 0.653 AC: 464031 AN: 710742 Hom.: 154387 Cov.: 9 AF XY: 0.649 AC XY: 242847 AN XY: 373964

African (AFR) AF: 0.418 AC: 7831 AN: 18752

American (AMR) AF: 0.494 AC: 17152 AN: 34724

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 13473 AN: 20900

East Asian (EAS) AF: 0.783 AC: 25430 AN: 32464

South Asian (SAS) AF: 0.547 AC: 35601 AN: 65100

European-Finnish (FIN) AF: 0.681 AC: 22847 AN: 33544

Middle Eastern (MID) AF: 0.665 AC: 2919 AN: 4392

European-Non Finnish (NFE) AF: 0.679 AC: 315649 AN: 465132

Other (OTH) AF: 0.647 AC: 23129 AN: 35734

GnomAD4 genome AF: 0.596 AC: 90480 AN: 151898 Hom.: 28079 Cov.: 31 AF XY: 0.595 AC XY: 44149 AN XY: 74234

African (AFR) AF: 0.430 AC: 17798 AN: 41412

American (AMR) AF: 0.552 AC: 8435 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2285 AN: 3470

East Asian (EAS) AF: 0.806 AC: 4146 AN: 5142

South Asian (SAS) AF: 0.550 AC: 2636 AN: 4796

European-Finnish (FIN) AF: 0.682 AC: 7201 AN: 10552

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46020 AN: 67942

Other (OTH) AF: 0.636 AC: 1343 AN: 2112

Alfa AF: 0.604 Hom.: 17752

Bravo AF: 0.581

Asia WGS AF: 0.644 AC: 2237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	10
DANN	Benign	0.79
PhyloP100		0.031
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: rs1417582; hg19: chr1-161696088; COSMIC: COSV61060126;