Variant rs3811035 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031281.3(FCRL5):c.2845-7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 1,613,542 control chromosomes in the GnomAD database, including 327,006 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.52 ( 23970 hom., cov: 32)

Exomes 𝑓: 0.64 ( 303036 hom. )

Consequence

FCRL5
NM_031281.3 splice_region, intron

Scores

Splicing: ADA: 0.00002593

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.455

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCRL5	NM_031281.3 link	c.2845-7C>T		splice_region_variant, intron_variant		ENST00000361835.8	NP_112571.2	Q96RD9-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
FCRL5	ENST00000361835.8 link	c.2845-7C>T	splice_region_variant, intron_variant	1	NM_031281.3	ENSP00000354691.3	Q96RD9-1
FCRL5	ENST00000461387.5 link	n.2122-7C>T	splice_region_variant, intron_variant	2
FCRL5	ENST00000462218.1 link	n.233-7C>T	splice_region_variant, intron_variant	2
FCRL5	ENST00000497286.5 link	n.1938-7C>T	splice_region_variant, intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.518

AC:

78579

AN:

151818

Hom.:

23959

Cov.:

show subpopulations

Gnomad AFR

AF:

0.168

Gnomad AMI

AF:

0.546

Gnomad AMR

AF:

0.638

Gnomad ASJ

AF:

0.621

Gnomad EAS

AF:

0.654

Gnomad SAS

AF:

0.688

Gnomad FIN

AF:

0.673

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.651

Gnomad OTH

AF:

0.531

GnomAD3 exomes

AF:

0.634

AC:

159414

AN:

251336

Hom.:

53016

AF XY:

0.642

AC XY:

87204

AN XY:

135876

show subpopulations

Gnomad AFR exome

AF:

0.151

Gnomad AMR exome

AF:

0.720

Gnomad ASJ exome

AF:

0.623

Gnomad EAS exome

AF:

0.653

Gnomad SAS exome

AF:

0.665

Gnomad FIN exome

AF:

0.690

Gnomad NFE exome

AF:

0.656

Gnomad OTH exome

AF:

0.648

GnomAD4 exome

AF:

0.638

AC:

932433

AN:

1461604

Hom.:

303036

Cov.:

AF XY:

0.640

AC XY:

465658

AN XY:

727120

show subpopulations

Gnomad4 AFR exome

AF:

0.145

Gnomad4 AMR exome

AF:

0.712

Gnomad4 ASJ exome

AF:

0.625

Gnomad4 EAS exome

AF:

0.656

Gnomad4 SAS exome

AF:

0.666

Gnomad4 FIN exome

AF:

0.687

Gnomad4 NFE exome

AF:

0.647

Gnomad4 OTH exome

AF:

0.612

GnomAD4 genome

AF:

0.517

AC:

78598

AN:

151938

Hom.:

23970

Cov.:

AF XY:

0.527

AC XY:

39110

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.167

Gnomad4 AMR

AF:

0.639

Gnomad4 ASJ

AF:

0.621

Gnomad4 EAS

AF:

0.654

Gnomad4 SAS

AF:

0.689

Gnomad4 FIN

AF:

0.673

Gnomad4 NFE

AF:

0.651

Gnomad4 OTH

AF:

0.528

Alfa

AF:

0.621

Hom.:

49105

Bravo

AF:

0.498

Asia WGS

AF:

0.630

AC:

2187

AN:

3478

EpiCase

AF:

0.640

EpiControl

AF:

0.638

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.6

DANN

Benign

0.46

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000026

dbscSNV1_RF

Benign

0.0

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over