dbSNP rs1332714: FCRL5:c.2660+17A>C (chr1-157519726-T-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.2660+17A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 1,610,896 control chromosomes in the GnomAD database, including 67,239 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 0.22 ( 4476 hom., cov: 32)

Exomes 𝑓: 0.29 ( 62763 hom. )

Consequence

FCRL5
NM_031281.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.481

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:

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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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 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.2660+17A>C		intron	N/A	NP_112571.2	Q96RD9-1
	FCRL5	NM_001195388.2		c.2660+17A>C		intron	N/A	NP_001182317.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FCRL5	ENST00000361835.8	TSL:1 MANE Select	c.2660+17A>C	intron	N/A	ENSP00000354691.3	Q96RD9-1
FCRL5	ENST00000908742.1		c.2543+17A>C	intron	N/A	ENSP00000578801.1
FCRL5	ENST00000461387.5	TSL:2	n.1937+17A>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.217

AC:

32974

AN:

152006

Hom.:

4473

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0558

Gnomad AMI

AF:

0.214

Gnomad AMR

AF:

0.230

Gnomad ASJ

AF:

0.385

Gnomad EAS

AF:

0.0978

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.233

GnomAD2 exomes

AF:

0.263

AC:

66103

AN:

251250

AF XY:

0.271

show subpopulations

Gnomad AFR exome

AF:

0.0466

Gnomad AMR exome

AF:

0.244

Gnomad ASJ exome

AF:

0.370

Gnomad EAS exome

AF:

0.0994

Gnomad FIN exome

AF:

0.269

Gnomad NFE exome

AF:

0.306

Gnomad OTH exome

AF:

0.297

GnomAD4 exome

AF:

0.287

AC:

418499

AN:

1458772

Hom.:

62763

Cov.:

AF XY:

0.289

AC XY:

209735

AN XY:

725928

show subpopulations

African (AFR)

AF:

0.0441

AC:

1473

AN:

33420

American (AMR)

AF:

0.242

AC:

10810

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.371

AC:

9682

AN:

26120

East Asian (EAS)

AF:

0.0939

AC:

3728

AN:

39690

South Asian (SAS)

AF:

0.302

AC:

26001

AN:

86170

European-Finnish (FIN)

AF:

0.273

AC:

14572

AN:

53414

Middle Eastern (MID)

AF:

0.342

AC:

1957

AN:

5720

European-Non Finnish (NFE)

AF:

0.301

AC:

333696

AN:

1109228

Other (OTH)

AF:

0.275

AC:

16580

AN:

60302

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

13913

27826

41740

55653

69566

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10818

21636

32454

43272

54090

<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:

0.217

AC:

32985

AN:

152124

Hom.:

4476

Cov.:

AF XY:

0.218

AC XY:

16231

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.0556

AC:

2311

AN:

41536

American (AMR)

AF:

0.230

AC:

3516

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.385

AC:

1332

AN:

3462

East Asian (EAS)

AF:

0.0982

AC:

508

AN:

5174

South Asian (SAS)

AF:

0.293

AC:

1409

AN:

4810

European-Finnish (FIN)

AF:

0.274

AC:

2891

AN:

10564

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.298

AC:

20250

AN:

67980

Other (OTH)

AF:

0.233

AC:

492

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1263

2526

3789

5052

6315

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

364

728

1092

1456

1820

<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:

0.274

Hom.:

5354

Bravo

AF:

0.207

Asia WGS

AF:

0.164

AC:

570

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

(source)

DANN

Benign

0.73

PhyloP100

0.48

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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