rs6427383

Variant names:

• chr1-157521383-T-A
• rs6427383
• NM_031281.3:c.2240-91A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-157521383-T-A
• chr1-157521383-T-C
• chr1-157521383-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031281.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRL5	NM_031281.3	MANE Select	c.2240-91A>T		intron	N/A	NP_112571.2
	FCRL5	NM_001195388.2		c.2240-91A>T		intron	N/A	NP_001182317.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRL5	ENST00000361835.8	TSL:1 MANE Select	c.2240-91A>T		intron	N/A	ENSP00000354691.3
	FCRL5	ENST00000461387.5	TSL:2	n.1412A>T		non_coding_transcript_exon	Exon 1 of 7
	FCRL5	ENST00000497286.5	TSL:2	n.1333-91A>T		intron	N/A

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

African (AFR) AF: 0.361 AC: 10067 AN: 27872

American (AMR) AF: 0.788 AC: 16588 AN: 21044

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 15746 AN: 18808

East Asian (EAS) AF: 0.761 AC: 27186 AN: 35746

South Asian (SAS) AF: 0.844 AC: 51938 AN: 61556

European-Finnish (FIN) AF: 0.856 AC: 38864 AN: 45376

Middle Eastern (MID) AF: 0.789 AC: 4057 AN: 5142

European-Non Finnish (NFE) AF: 0.799 AC: 797009 AN: 997690

Other (OTH) AF: 0.775 AC: 40849 AN: 52684

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

African (AFR) AF: 0.382 AC: 15851 AN: 41466

American (AMR) AF: 0.757 AC: 11584 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2916 AN: 3470

East Asian (EAS) AF: 0.775 AC: 4024 AN: 5192

South Asian (SAS) AF: 0.845 AC: 4083 AN: 4832

European-Finnish (FIN) AF: 0.857 AC: 9085 AN: 10598

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54813 AN: 68006

Other (OTH) AF: 0.720 AC: 1520 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.67
PhyloP100		0.59
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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