rs6427383

chr1-157521383-T-Achr1-157521383-T-C

Variant summary

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

The NM_031281.3(FCRL5):c.2240-91A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 1,418,094 control chromosomes in the GnomAD database, including 439,064 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 0.69 (38902 hom., cov: 33)
  • Exomes 𝑓: 0.79 (400162 hom.)
• Consequence: FCRL5 NM_031281.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

Genes affected

FCRL5 (HGNC:18508): (Fc receptor like 5) This gene encodes a member of the immunoglobulin receptor superfamily and the Fc-receptor like family. This gene and several other Fc receptor-like gene members are clustered on the long arm of chromosome 1. The encoded protein is a single-pass type I membrane protein and contains 8 immunoglobulin-like C2-type domains. This gene is implicated in B cell development and lymphomagenesis. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Sep 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCRL5	NM_031281.3	c.2240-91A>T		intron_variant		ENST00000361835.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCRL5	ENST00000361835.8	c.2240-91A>T		intron_variant		1	NM_031281.3	P1
FCRL5	ENST00000461387.5	n.1412A>T		non_coding_transcript_exon_variant	1/7	2
FCRL5	ENST00000497286.5	n.1333-91A>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104801 AN: 152058 Hom.: 38904 Cov.: 33

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.721

GnomAD4 exome AF: 0.792 AC: 1002304 AN: 1265918 Hom.: 400162 Cov.: 18 AF XY: 0.794 AC XY: 490876 AN XY: 618006

Gnomad4 AFR exome AF: 0.361

Gnomad4 AMR exome AF: 0.788

Gnomad4 ASJ exome AF: 0.837

Gnomad4 EAS exome AF: 0.761

Gnomad4 SAS exome AF: 0.844

Gnomad4 FIN exome AF: 0.856

Gnomad4 NFE exome AF: 0.799

Gnomad4 OTH exome AF: 0.775

GnomAD4 genome AF: 0.689 AC: 104817 AN: 152176 Hom.: 38902 Cov.: 33 AF XY: 0.695 AC XY: 51720 AN XY: 74410

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.720

Alfa AF: 0.744 Hom.: 5486

Bravo AF: 0.667

Asia WGS AF: 0.773 AC: 2688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.1
Dann	Benign	0.67

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: rs6427383; hg19: chr1-157491173; COSMIC: COSV62521791; COSMIC: COSV62521791;