dbSNP rs17416676: FCRL5:c.*501C>T (chr1-157534015-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 ENST00000368189.3(FCRL5):c.*501C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 178,768 control chromosomes in the GnomAD database, including 5,154 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 0.21 ( 4281 hom., cov: 32)

Exomes 𝑓: 0.25 ( 873 hom. )

Consequence

FCRL5
ENST00000368189.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.278

Publications

7 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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCRL5	NM_031281.3 link	c.1681+599C>T		intron_variant	Intron 8 of 16	ENST00000361835.8	NP_112571.2	Q96RD9-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
FCRL5	ENST00000368189.3 link	c.*501C>T	3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000357172.3	Q96RD9-4
FCRL5	ENST00000361835.8 link	c.1681+599C>T	intron_variant	Intron 8 of 16	1	NM_031281.3	ENSP00000354691.3	Q96RD9-1
FCRL5	ENST00000368190.7 link	c.1681+599C>T	intron_variant	Intron 8 of 9	1		ENSP00000357173.3	Q96RD9-3

Frequencies

GnomAD3 genomes

AF:

0.212

AC:

32230

AN:

151948

Hom.:

4279

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0526

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.422

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.277

Gnomad FIN

AF:

0.256

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.232

GnomAD4 exome

AF:

0.249

AC:

6644

AN:

26702

Hom.:

873

Cov.:

AF XY:

0.243

AC XY:

3403

AN XY:

13996

show subpopulations

African (AFR)

AF:

0.0460

AC:

AN:

544

American (AMR)

AF:

0.220

AC:

606

AN:

2754

Ashkenazi Jewish (ASJ)

AF:

0.372

AC:

221

AN:

594

East Asian (EAS)

AF:

0.0928

AC:

146

AN:

1574

South Asian (SAS)

AF:

0.276

AC:

856

AN:

3106

European-Finnish (FIN)

AF:

0.249

AC:

266

AN:

1070

Middle Eastern (MID)

AF:

0.273

AC:

AN:

European-Non Finnish (NFE)

AF:

0.265

AC:

4164

AN:

15690

Other (OTH)

AF:

0.262

AC:

342

AN:

1304

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

244

488

732

976

1220

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

116

174

232

290

<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:

0.212

AC:

32235

AN:

152066

Hom.:

4281

Cov.:

AF XY:

0.212

AC XY:

15794

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.0524

AC:

2176

AN:

41494

American (AMR)

AF:

0.228

AC:

3487

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.422

AC:

1461

AN:

3464

East Asian (EAS)

AF:

0.106

AC:

549

AN:

5182

South Asian (SAS)

AF:

0.277

AC:

1335

AN:

4824

European-Finnish (FIN)

AF:

0.256

AC:

2698

AN:

10558

Middle Eastern (MID)

AF:

0.255

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.291

AC:

19795

AN:

67950

Other (OTH)

AF:

0.233

AC:

490

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1224

2448

3671

4895

6119

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

358

716

1074

1432

1790

<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:

0.265

Hom.:

5940

Bravo

AF:

0.204

Asia WGS

AF:

0.154

AC:

534

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

5.6

(source)

DANN

Benign

0.50

PhyloP100

0.28

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