chr1-161723213-T-C

Variant names:

• chr1-161723213-T-C
• rs4657093
• NM_001002901.4:c.53-154T>C

Variant summary

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

The NM_001002901.4(FCRLB):​c.53-154T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,026 control chromosomes in the GnomAD database, including 2,848 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 0.18 (2848 hom., cov: 31)
• Consequence: FCRLB NM_001002901.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 10 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCRLB	NM_001002901.4	c.53-154T>C		intron_variant	Intron 4 of 7	ENST00000367948.7	NP_001002901.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCRLB	ENST00000367948.7	c.53-154T>C		intron_variant	Intron 4 of 7	1	NM_001002901.4	ENSP00000356925.2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27465 AN: 151908 Hom.: 2833 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.181 AC: 27502 AN: 152026 Hom.: 2848 Cov.: 31 AF XY: 0.182 AC XY: 13548 AN XY: 74308

African (AFR) AF: 0.224 AC: 9269 AN: 41412

American (AMR) AF: 0.310 AC: 4732 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3470

East Asian (EAS) AF: 0.149 AC: 771 AN: 5158

South Asian (SAS) AF: 0.120 AC: 581 AN: 4822

European-Finnish (FIN) AF: 0.155 AC: 1637 AN: 10588

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9229 AN: 67992

Other (OTH) AF: 0.197 AC: 416 AN: 2110

Alfa AF: 0.164 Hom.: 3933

Bravo AF: 0.199

Asia WGS AF: 0.185 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.41
DANN	Benign	0.70
PhyloP100		-0.072
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs4657093; hg19: chr1-161693003; COSMIC: COSV61060211; COSMIC: COSV61060211;