1-157576556-T-A

Position:

• chr1-157576556-T-A

Variant summary

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

The NM_031282.3(FCRL4):​c.1430-826A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,064 control chromosomes in the GnomAD database, including 17,881 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 0.45 (17881 hom., cov: 32)
• Consequence: FCRL4 NM_031282.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCRL4	NM_031282.3	c.1430-826A>T		intron_variant		ENST00000271532.2	NP_112572.1
FCRL4	XM_011510034.2	c.1427-826A>T		intron_variant			XP_011508336.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCRL4	ENST00000271532.2	c.1430-826A>T		intron_variant		1	NM_031282.3	ENSP00000271532.1
FCRL4	ENST00000448509.6	n.1398-826A>T		intron_variant		2
FCRL4	ENST00000479869.1	n.370-826A>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68704 AN: 151946 Hom.: 17855 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.452 AC: 68774 AN: 152064 Hom.: 17881 Cov.: 32 AF XY: 0.446 AC XY: 33156 AN XY: 74348

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.443

Alfa AF: 0.389 Hom.: 1558

Bravo AF: 0.467

Asia WGS AF: 0.314 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.65

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: rs849826; hg19: chr1-157546346;