Genetic Variant CXCR5:c.52-254C>T (chr11-118893342-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001716.5(CXCR5):c.52-254C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 972,114 control chromosomes in the GnomAD database, including 38,143 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 0.33 ( 9035 hom., cov: 32)

Exomes 𝑓: 0.26 ( 29108 hom. )

Consequence

CXCR5
NM_001716.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.710

Publications

17 publications found

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:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001716.5. 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
	CXCR5	NM_001716.5	MANE Select	c.52-254C>T		intron	N/A	NP_001707.1	P32302-1
	CXCR5	NM_032966.2		c.-338C>T		upstream_gene	N/A	NP_116743.1	P32302-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCR5	ENST00000292174.5	TSL:1 MANE Select	c.52-254C>T		intron	N/A	ENSP00000292174.4	P32302-1

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

50386

AN:

151938

Hom.:

8996

Cov.:

show subpopulations

Gnomad AFR

AF:

0.445

Gnomad AMI

AF:

0.259

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.239

Gnomad EAS

AF:

0.212

Gnomad SAS

AF:

0.164

Gnomad FIN

AF:

0.312

Gnomad MID

AF:

0.188

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.309

GnomAD4 exome

AF:

0.263

AC:

215818

AN:

820058

Hom.:

29108

Cov.:

AF XY:

0.263

AC XY:

99557

AN XY:

379204

show subpopulations

African (AFR)

AF:

0.446

AC:

6891

AN:

15440

American (AMR)

AF:

0.443

AC:

430

AN:

970

Ashkenazi Jewish (ASJ)

AF:

0.235

AC:

1198

AN:

5088

East Asian (EAS)

AF:

0.230

AC:

823

AN:

3572

South Asian (SAS)

AF:

0.176

AC:

2841

AN:

16180

European-Finnish (FIN)

AF:

0.255

AC:

AN:

274

Middle Eastern (MID)

AF:

0.232

AC:

369

AN:

1592

European-Non Finnish (NFE)

AF:

0.262

AC:

196205

AN:

750098

Other (OTH)

AF:

0.260

AC:

6991

AN:

26844

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

7480

14959

22439

29918

37398

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9044

18088

27132

36176

45220

<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:

0.332

AC:

50474

AN:

152056

Hom.:

9035

Cov.:

AF XY:

0.335

AC XY:

24866

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.446

AC:

18481

AN:

41438

American (AMR)

AF:

0.432

AC:

6603

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.239

AC:

828

AN:

3468

East Asian (EAS)

AF:

0.212

AC:

1100

AN:

5182

South Asian (SAS)

AF:

0.164

AC:

791

AN:

4826

European-Finnish (FIN)

AF:

0.312

AC:

3303

AN:

10572

Middle Eastern (MID)

AF:

0.178

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.271

AC:

18434

AN:

67976

Other (OTH)

AF:

0.306

AC:

646

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1697

3395

5092

6790

8487

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

478

956

1434

1912

2390

<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:

0.342

Hom.:

6779

Bravo

AF:

0.347

Asia WGS

AF:

0.180

AC:

627

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.98

(source)

DANN

Benign

0.54

PhyloP100

-0.71

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over