1-161726298-T-C

Position:

• chr1-161726298-T-C

Variant summary

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

The ENST00000367948.7(FCRLB):​c.574+211T>C variant causes a intron 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 ENST00000367948.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCRLB	NM_001002901.4	c.574+211T>C		intron_variant		ENST00000367948.7	NP_001002901.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCRLB	ENST00000367948.7	c.574+211T>C		intron_variant		1	NM_001002901.4	ENSP00000356925	P1

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

GnomAD3 exomes AF: 0.618 AC: 84043 AN: 136092 Hom.: 26887 AF XY: 0.618 AC XY: 45577 AN XY: 73696

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 SAS exome AF: 0.545

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

Gnomad4 AFR exome AF: 0.418

Gnomad4 AMR exome AF: 0.494

Gnomad4 ASJ exome AF: 0.645

Gnomad4 EAS exome AF: 0.783

Gnomad4 SAS exome AF: 0.547

Gnomad4 FIN exome AF: 0.681

Gnomad4 NFE exome AF: 0.679

Gnomad4 OTH exome AF: 0.647

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

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.636

Alfa AF: 0.631 Hom.: 14402

Bravo AF: 0.581

Asia WGS AF: 0.644 AC: 2237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	10
DANN	Benign	0.79

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: rs1417582; hg19: chr1-161696088; COSMIC: COSV61060126;