dbSNP rs3811036: FCRL5:c.*190A>C (chr1-157515485-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.*190A>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 0.0968 in 1,272,072 control chromosomes in the GnomAD database, including 10,658 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 0.18 ( 4280 hom., cov: 33)

Exomes 𝑓: 0.086 ( 6378 hom. )

Consequence

FCRL5
NM_031281.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.638

Publications

10 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCRL5	NM_031281.3 link	c.*190A>C		3_prime_UTR_variant	Exon 17 of 17	ENST00000361835.8	NP_112571.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
FCRL5	ENST00000361835.8 link	c.*190A>C	3_prime_UTR_variant	Exon 17 of 17	1	NM_031281.3	ENSP00000354691.3
FCRL5	ENST00000461387.5 link	n.2401A>C	non_coding_transcript_exon_variant	Exon 7 of 7	2
FCRL5	ENST00000462218.1 link	n.512A>C	non_coding_transcript_exon_variant	Exon 2 of 2	2
FCRL5	ENST00000497286.5 link	n.2217A>C	non_coding_transcript_exon_variant	Exon 9 of 9	2

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

27011

AN:

152090

Hom.:

4278

Cov.:

show subpopulations

Gnomad AFR

AF:

0.431

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.0712

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.0570

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0746

Gnomad OTH

AF:

0.161

GnomAD4 exome

AF:

0.0858

AC:

96122

AN:

1119864

Hom.:

6378

Cov.:

AF XY:

0.0863

AC XY:

48192

AN XY:

558424

show subpopulations

African (AFR)

AF:

0.453

AC:

11776

AN:

26016

American (AMR)

AF:

0.0764

AC:

2212

AN:

28946

Ashkenazi Jewish (ASJ)

AF:

0.0731

AC:

1431

AN:

19584

East Asian (EAS)

AF:

0.101

AC:

3650

AN:

36182

South Asian (SAS)

AF:

0.128

AC:

8474

AN:

65960

European-Finnish (FIN)

AF:

0.0533

AC:

1916

AN:

35932

Middle Eastern (MID)

AF:

0.130

AC:

565

AN:

4360

European-Non Finnish (NFE)

AF:

0.0714

AC:

60992

AN:

854578

Other (OTH)

AF:

0.106

AC:

5106

AN:

48306

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

4153

8306

12458

16611

20764

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2316

4632

6948

9264

11580

<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:

0.178

AC:

27047

AN:

152208

Hom.:

4280

Cov.:

AF XY:

0.174

AC XY:

12945

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.430

AC:

17862

AN:

41504

American (AMR)

AF:

0.107

AC:

1638

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0712

AC:

247

AN:

3470

East Asian (EAS)

AF:

0.119

AC:

614

AN:

5172

South Asian (SAS)

AF:

0.117

AC:

563

AN:

4818

European-Finnish (FIN)

AF:

0.0570

AC:

605

AN:

10618

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0746

AC:

5073

AN:

68010

Other (OTH)

AF:

0.162

AC:

341

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

975

1950

2925

3900

4875

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

264

528

792

1056

1320

<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:

0.106

Hom.:

1447

Bravo

AF:

0.193

Asia WGS

AF:

0.145

AC:

503

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

3.3

(source)

DANN

Benign

0.61

PhyloP100

0.64

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