dbSNP rs10494316: FCRL5:c.844+483C>T (chr1-157543779-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_031281.3(FCRL5):c.844+483C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,024 control chromosomes in the GnomAD database, including 27,051 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 0.58 ( 27051 hom., cov: 32)

Consequence

FCRL5
NM_031281.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.27

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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new If you want to explore the variant's impact on the transcript NM_031281.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-1.02).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.737 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.844+483C>T		intron	N/A	NP_112571.2	Q96RD9-1
	FCRL5	NM_001195388.2		c.844+483C>T		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.844+483C>T	intron	N/A	ENSP00000354691.3	Q96RD9-1
FCRL5	ENST00000368190.7	TSL:1	c.844+483C>T	intron	N/A	ENSP00000357173.3	Q96RD9-3
FCRL5	ENST00000368189.3	TSL:1	c.844+483C>T	intron	N/A	ENSP00000357172.3	Q96RD9-4

Frequencies

GnomAD3 genomes

AF:

0.583

AC:

88495

AN:

151906

Hom.:

27037

Cov.:

show subpopulations

Gnomad AFR

AF:

0.386

Gnomad AMI

AF:

0.567

Gnomad AMR

AF:

0.648

Gnomad ASJ

AF:

0.654

Gnomad EAS

AF:

0.728

Gnomad SAS

AF:

0.758

Gnomad FIN

AF:

0.678

Gnomad MID

AF:

0.538

Gnomad NFE

AF:

0.646

Gnomad OTH

AF:

0.577

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.582

AC:

88540

AN:

152024

Hom.:

27051

Cov.:

AF XY:

0.590

AC XY:

43807

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.386

AC:

15979

AN:

41438

American (AMR)

AF:

0.649

AC:

9912

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.654

AC:

2269

AN:

3470

East Asian (EAS)

AF:

0.728

AC:

3763

AN:

5168

South Asian (SAS)

AF:

0.757

AC:

3649

AN:

4818

European-Finnish (FIN)

AF:

0.678

AC:

7164

AN:

10574

Middle Eastern (MID)

AF:

0.541

AC:

159

AN:

294

European-Non Finnish (NFE)

AF:

0.646

AC:

43912

AN:

67960

Other (OTH)

AF:

0.576

AC:

1216

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1793

3586

5378

7171

8964

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

748

1496

2244

2992

3740

<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:

0.629

Hom.:

52522

Bravo

AF:

0.568

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

-1.0

CADD

Benign

0.23

(source)

DANN

Benign

0.22

PhyloP100

-3.3

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over