dbSNP rs10489674: FCRL4:c.52+99C>T (chr1-157596229-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_031282.3(FCRL4):c.52+99C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 1,336,152 control chromosomes in the GnomAD database, including 71,834 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 0.31 ( 7312 hom., cov: 32)

Exomes 𝑓: 0.33 ( 64522 hom. )

Consequence

FCRL4
NM_031282.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0850

Publications

13 publications found

Variant links:

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 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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCRL4	NM_031282.3 link	c.52+99C>T		intron_variant	Intron 2 of 11	ENST00000271532.2	NP_112572.1	Q96PJ5-1
FCRL4	XM_011510034.2 link	c.52+99C>T		intron_variant	Intron 2 of 11		XP_011508336.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCRL4	ENST00000271532.2 link	c.52+99C>T		intron_variant	Intron 2 of 11	1	NM_031282.3	ENSP00000271532.1		Q96PJ5-1

Frequencies

GnomAD3 genomes

AF:

0.308

AC:

46813

AN:

151896

Hom.:

7295

Cov.:

show subpopulations

Gnomad AFR

AF:

0.287

Gnomad AMI

AF:

0.383

Gnomad AMR

AF:

0.312

Gnomad ASJ

AF:

0.259

Gnomad EAS

AF:

0.220

Gnomad SAS

AF:

0.298

Gnomad FIN

AF:

0.287

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.338

GnomAD4 exome

AF:

0.327

AC:

386972

AN:

1184138

Hom.:

64522

AF XY:

0.327

AC XY:

195956

AN XY:

600110

show subpopulations

African (AFR)

AF:

0.287

AC:

7945

AN:

27728

American (AMR)

AF:

0.261

AC:

10826

AN:

41492

Ashkenazi Jewish (ASJ)

AF:

0.257

AC:

6108

AN:

23728

East Asian (EAS)

AF:

0.221

AC:

8346

AN:

37764

South Asian (SAS)

AF:

0.323

AC:

25064

AN:

77608

European-Finnish (FIN)

AF:

0.282

AC:

14456

AN:

51226

Middle Eastern (MID)

AF:

0.371

AC:

1784

AN:

4806

European-Non Finnish (NFE)

AF:

0.340

AC:

295655

AN:

868852

Other (OTH)

AF:

0.330

AC:

16788

AN:

50934

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

12349

24698

37047

49396

61745

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8642

17284

25926

34568

43210

<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:

0.308

AC:

46877

AN:

152014

Hom.:

7312

Cov.:

AF XY:

0.306

AC XY:

22761

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.288

AC:

11933

AN:

41446

American (AMR)

AF:

0.312

AC:

4761

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.259

AC:

897

AN:

3468

East Asian (EAS)

AF:

0.220

AC:

1138

AN:

5184

South Asian (SAS)

AF:

0.300

AC:

1442

AN:

4810

European-Finnish (FIN)

AF:

0.287

AC:

3032

AN:

10566

Middle Eastern (MID)

AF:

0.391

AC:

115

AN:

294

European-Non Finnish (NFE)

AF:

0.331

AC:

22486

AN:

67954

Other (OTH)

AF:

0.343

AC:

724

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1682

3364

5045

6727

8409

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

484

968

1452

1936

2420

<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:

0.313

Hom.:

1241

Bravo

AF:

0.310

Asia WGS

AF:

0.303

AC:

1055

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.3

(source)

DANN

Benign

0.57

PhyloP100

0.085

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over