Variant chr1-161673236-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_001394477.1(FCGR2B):c.646+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000325 in 1,590,370 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00031 ( 1 hom., cov: 30)

Exomes 𝑓: 0.00033 ( 5 hom. )

Consequence

FCGR2B
NM_001394477.1 splice_region, intron

Scores

Splicing: ADA: 0.00003317

Clinical Significance

Likely benign no assertion criteria provided B:2

Conservation

PhyloP100: -0.0570

Variant links:

Genes affected

FCGR2B (HGNC:3618): (Fc gamma receptor IIb) The protein encoded by this gene is a low affinity receptor for the Fc region of immunoglobulin gamma complexes. The encoded protein is involved in the phagocytosis of immune complexes and in the regulation of antibody production by B-cells. Variations in this gene may increase susceptibilty to systemic lupus erythematosus (SLE). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]

FCGR2B links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 1-161673236-G-A is Benign according to our data. Variant chr1-161673236-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1285216.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-161673236-G-A is described in Lovd as [Likely_benign].

BS2

High Homozygotes in GnomAdExome4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCGR2B	NM_001394477.1 linkuse as main transcript	c.646+7G>A		splice_region_variant, intron_variant		ENST00000358671.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCGR2B	ENST00000358671.10 linkuse as main transcript	c.646+7G>A		splice_region_variant, intron_variant		1	NM_001394477.1	P4	P31994-1
	ENST00000453111.1 linkuse as main transcript	n.198-953C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.000302

AC:

AN:

149024

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000750

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000203

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00526

Gnomad SAS

AF:

0.000216

Gnomad FIN

AF:

0.000193

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000104

Gnomad OTH

AF:

0.000972

GnomAD3 exomes

AF:

0.000542

AC:

128

AN:

236230

Hom.:

AF XY:

0.000526

AC XY:

AN XY:

127376

show subpopulations

Gnomad AFR exome

AF:

0.0000664

Gnomad AMR exome

AF:

0.0000627

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00558

Gnomad SAS exome

AF:

0.0000723

Gnomad FIN exome

AF:

0.000241

Gnomad NFE exome

AF:

0.000157

Gnomad OTH exome

AF:

0.000348

GnomAD4 exome

AF:

0.000327

AC:

471

AN:

1441234

Hom.:

Cov.:

AF XY:

0.000317

AC XY:

227

AN XY:

715600

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000709

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00801

Gnomad4 SAS exome

AF:

0.0000120

Gnomad4 FIN exome

AF:

0.000151

Gnomad4 NFE exome

AF:

0.0000954

Gnomad4 OTH exome

AF:

0.000639

GnomAD4 genome

AF:

0.000308

AC:

AN:

149136

Hom.:

Cov.:

AF XY:

0.000275

AC XY:

AN XY:

72694

show subpopulations

Gnomad4 AFR

AF:

0.0000748

Gnomad4 AMR

AF:

0.000203

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00528

Gnomad4 SAS

AF:

0.000216

Gnomad4 FIN

AF:

0.000193

Gnomad4 NFE

AF:

0.000104

Gnomad4 OTH

AF:

0.00144

Alfa

AF:

0.000219

Hom.:

Bravo

AF:

0.000257

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000033

dbscSNV1_RF

Benign

0.0040

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over