Variant rs676925 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001716.5(CXCR5):c.*316C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 300,020 control chromosomes in the GnomAD database, including 8,263 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 0.20 ( 4160 hom., cov: 32)

Exomes 𝑓: 0.22 ( 4103 hom. )

Consequence

CXCR5
NM_001716.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0740

Variant links:

Genes affected

CXCR5 (HGNC:1060): (C-X-C motif chemokine receptor 5) This gene encodes a multi-pass membrane protein that belongs to the CXC chemokine receptor family. It is expressed in mature B-cells and Burkitt's lymphoma. This cytokine receptor binds to B-lymphocyte chemoattractant (BLC), and is involved in B-cell migration into B-cell follicles of spleen and Peyer patches. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

CXCR5 links:

BCL9L (HGNC:23688): (BCL9 like) Enables beta-catenin binding activity. Involved in several processes, including negative regulation of transforming growth factor beta receptor signaling pathway; positive regulation of epithelial to mesenchymal transition; and positive regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Apr 2022]

BCL9L links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CXCR5	NM_001716.5 linkuse as main transcript	c.*316C>G		3_prime_UTR_variant	2/2	ENST00000292174.5	NP_001707.1
CXCR5	NM_032966.2 linkuse as main transcript	c.*316C>G		3_prime_UTR_variant	1/1		NP_116743.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CXCR5	ENST00000292174.5 linkuse as main transcript	c.*316C>G		3_prime_UTR_variant	2/2	1	NM_001716.5	ENSP00000292174	P1	P32302-1
BCL9L	ENST00000334801.7 linkuse as main transcript	c.*3436G>C		3_prime_UTR_variant	8/8	1		ENSP00000335320	P4	Q86UU0-1

Frequencies

GnomAD3 genomes

AF:

0.205

AC:

31109

AN:

152022

Hom.:

4147

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0622

Gnomad AMI

AF:

0.255

Gnomad AMR

AF:

0.372

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.144

Gnomad FIN

AF:

0.259

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.257

Gnomad OTH

AF:

0.211

GnomAD4 exome

AF:

0.221

AC:

32618

AN:

147880

Hom.:

4103

Cov.:

AF XY:

0.221

AC XY:

16344

AN XY:

73940

show subpopulations

Gnomad4 AFR exome

AF:

0.0627

Gnomad4 AMR exome

AF:

0.382

Gnomad4 ASJ exome

AF:

0.194

Gnomad4 EAS exome

AF:

0.0541

Gnomad4 SAS exome

AF:

0.133

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.238

Gnomad4 OTH exome

AF:

0.225

GnomAD4 genome

AF:

0.205

AC:

31135

AN:

152140

Hom.:

4160

Cov.:

AF XY:

0.207

AC XY:

15386

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.0622

Gnomad4 AMR

AF:

0.373

Gnomad4 ASJ

AF:

0.205

Gnomad4 EAS

AF:

0.106

Gnomad4 SAS

AF:

0.144

Gnomad4 FIN

AF:

0.259

Gnomad4 NFE

AF:

0.256

Gnomad4 OTH

AF:

0.209

Alfa

AF:

0.229

Hom.:

661

Bravo

AF:

0.208

Asia WGS

AF:

0.115

AC:

400

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.2

DANN

Benign

0.54

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

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