1-161726298-T-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000495397.1(FCRLB):​n.398T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).

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>A		intron	N/A	NP_001002901.1
	FCRLB	NM_001320241.1		c.574+211T>A		intron	N/A	NP_001307170.1
	FCRLB	NM_001288829.1		c.574+211T>A		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>A		non_coding_transcript_exon	Exon 1 of 2
	FCRLB	ENST00000367948.7	TSL:1 MANE Select	c.574+211T>A		intron	N/A	ENSP00000356925.2
	FCRLB	ENST00000367946.7	TSL:1	c.574+211T>A		intron	N/A	ENSP00000356923.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 711776 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 374478

African (AFR) AF: 0.00 AC: 0 AN: 18770

American (AMR) AF: 0.00 AC: 0 AN: 34736

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20914

East Asian (EAS) AF: 0.00 AC: 0 AN: 32484

South Asian (SAS) AF: 0.00 AC: 0 AN: 65120

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33570

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4398

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 465994

Other (OTH) AF: 0.00 AC: 0 AN: 35790

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 17752

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.4
DANN	Benign	0.85
PhyloP100		0.031

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;