rs11264825

Positions:

• chr1-157818480-A-G

Variant summary

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

The NM_052938.5(FCRL1):​c.31+1527T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151,728 control chromosomes in the GnomAD database, including 15,034 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 0.44 (15034 hom., cov: 30)
• Consequence: FCRL1 NM_052938.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

FCRL1 (HGNC:18509): (Fc receptor like 1) This gene encodes a member of the immunoglobulin receptor superfamily and is one of several Fc receptor-like glycoproteins clustered on the long arm of chromosome 1. The encoded protein contains three extracellular C2-like immunoglobulin domains, a transmembrane domain and a cytoplasmic domain with two immunoreceptor-tyrosine activation motifs. This protein may play a role in the regulation of cancer cell growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCRL1	NM_052938.5	c.31+1527T>C		intron_variant		ENST00000368176.8	NP_443170.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCRL1	ENST00000368176.8	c.31+1527T>C		intron_variant		1	NM_052938.5	ENSP00000357158	P4

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66772 AN: 151616 Hom.: 15023 Cov.: 30

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.440 AC: 66817 AN: 151728 Hom.: 15034 Cov.: 30 AF XY: 0.436 AC XY: 32307 AN XY: 74138

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.455

Alfa AF: 0.416 Hom.: 2767

Bravo AF: 0.452

Asia WGS AF: 0.374 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.55

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: rs11264825; hg19: chr1-157788270;