chr1-157575060-C-T

Position:

• chr1-157575060-C-T

Variant summary

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

The NM_031282.3(FCRL4):​c.*464G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 253,318 control chromosomes in the GnomAD database, including 19,239 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 0.33 (10177 hom., cov: 33)
  • Exomes 𝑓: 0.40 (9062 hom.)
• Consequence: FCRL4 NM_031282.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373

Genes affected

FCRL4 (HGNC:18507): (Fc receptor like 4) 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 has four extracellular C2-type immunoglobulin domains, a transmembrane domain and a cytoplasmic domain that contains three immune-receptor tyrosine-based inhibitory motifs. This protein may play a role in the function of memory B-cells in the epithelia. Aberrations in the chromosomal region encoding this gene are associated with non-Hodgkin lymphoma and multiple myeloma. [provided by RefSeq, Apr 2009]

FCRL4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCRL4	NM_031282.3	c.*464G>A		3_prime_UTR_variant	12/12	ENST00000271532.2	NP_112572.1
FCRL4	XM_011510034.2	c.*464G>A		3_prime_UTR_variant	12/12		XP_011508336.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCRL4	ENST00000271532.2	c.*464G>A		3_prime_UTR_variant	12/12	1	NM_031282.3	ENSP00000271532.1
FCRL4	ENST00000448509.6	n.1980G>A		non_coding_transcript_exon_variant	9/9	2

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49891 AN: 152004 Hom.: 10173 Cov.: 33

Gnomad AFR AF: 0.0846

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.342

GnomAD4 exome AF: 0.405 AC: 40946 AN: 101196 Hom.: 9062 Cov.: 0 AF XY: 0.405 AC XY: 19499 AN XY: 48102

Gnomad4 AFR exome AF: 0.0806

Gnomad4 AMR exome AF: 0.519

Gnomad4 ASJ exome AF: 0.373

Gnomad4 EAS exome AF: 0.600

Gnomad4 SAS exome AF: 0.472

Gnomad4 FIN exome AF: 0.435

Gnomad4 NFE exome AF: 0.381

Gnomad4 OTH exome AF: 0.371

GnomAD4 genome AF: 0.328 AC: 49895 AN: 152122 Hom.: 10177 Cov.: 33 AF XY: 0.338 AC XY: 25137 AN XY: 74360

Gnomad4 AFR AF: 0.0844

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.338

Alfa AF: 0.382 Hom.: 11474

Bravo AF: 0.316

Asia WGS AF: 0.516 AC: 1794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.52

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: rs14335; hg19: chr1-157544850;