dbSNP rs3843307: FCRL5:c.*890T>C (chr1-157514785-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031281.3(FCRL5):c.*890T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,148 control chromosomes in the GnomAD database, including 30,210 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 0.61 ( 30200 hom., cov: 33)

Exomes 𝑓: 0.68 ( 10 hom. )

Consequence

FCRL5
NM_031281.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.630

Publications

9 publications found

Variant links:

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]

FCRL5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 = 0.771 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCRL5	NM_031281.3	MANE Select	c.*890T>C		3_prime_UTR	Exon 17 of 17	NP_112571.2
	FCRL5	NM_001195388.2		c.*817T>C		3_prime_UTR	Exon 17 of 17	NP_001182317.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FCRL5	ENST00000361835.8	TSL:1 MANE Select	c.*890T>C	3_prime_UTR	Exon 17 of 17	ENSP00000354691.3
FCRL5	ENST00000908742.1		c.*890T>C	3_prime_UTR	Exon 16 of 16	ENSP00000578801.1
FCRL5	ENST00000461387.5	TSL:2	n.3101T>C	non_coding_transcript_exon	Exon 7 of 7

Frequencies

GnomAD3 genomes

AF:

0.615

AC:

93449

AN:

151986

Hom.:

30192

Cov.:

show subpopulations

Gnomad AFR

AF:

0.406

Gnomad AMI

AF:

0.560

Gnomad AMR

AF:

0.699

Gnomad ASJ

AF:

0.715

Gnomad EAS

AF:

0.791

Gnomad SAS

AF:

0.683

Gnomad FIN

AF:

0.726

Gnomad MID

AF:

0.599

Gnomad NFE

AF:

0.683

Gnomad OTH

AF:

0.621

GnomAD4 exome

AF:

0.682

AC:

AN:

Hom.:

Cov.:

AF XY:

0.658

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.700

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.615

AC:

93483

AN:

152104

Hom.:

30200

Cov.:

AF XY:

0.622

AC XY:

46240

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.405

AC:

16802

AN:

41462

American (AMR)

AF:

0.700

AC:

10706

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.715

AC:

2478

AN:

3468

East Asian (EAS)

AF:

0.791

AC:

4105

AN:

5188

South Asian (SAS)

AF:

0.683

AC:

3294

AN:

4822

European-Finnish (FIN)

AF:

0.726

AC:

7683

AN:

10586

Middle Eastern (MID)

AF:

0.596

AC:

174

AN:

292

European-Non Finnish (NFE)

AF:

0.683

AC:

46429

AN:

67970

Other (OTH)

AF:

0.616

AC:

1302

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1724

3448

5171

6895

8619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

766

1532

2298

3064

3830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.660

Hom.:

116235

Bravo

AF:

0.602

Asia WGS

AF:

0.708

AC:

2461

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

4.7

(source)

DANN

Benign

0.47

PhyloP100

0.63

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over