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GeneBe

11-118893589-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001716.5(CXCR5):c.52-7C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00392 in 1,568,718 control chromosomes in the GnomAD database, including 195 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.021 ( 112 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 83 hom. )

Consequence

CXCR5
NM_001716.5 splice_region, splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.03682
2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.364
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
Variant 11-118893589-C-G is Benign according to our data. Variant chr11-118893589-C-G is described in ClinVar as [Benign]. Clinvar id is 789043.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0705 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CXCR5NM_001716.5 linkuse as main transcriptc.52-7C>G splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000292174.5
CXCR5NM_032966.2 linkuse as main transcriptc.-91C>G 5_prime_UTR_variant 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CXCR5ENST00000292174.5 linkuse as main transcriptc.52-7C>G splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_001716.5 P1P32302-1

Frequencies

GnomAD3 genomes
AF:
0.0211
AC:
3211
AN:
152196
Hom.:
112
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0107
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000220
Gnomad OTH
AF:
0.0139
GnomAD3 exomes
AF:
0.00584
AC:
1316
AN:
225514
Hom.:
41
AF XY:
0.00422
AC XY:
511
AN XY:
121188
show subpopulations
Gnomad AFR exome
AF:
0.0725
Gnomad AMR exome
AF:
0.00400
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000560
Gnomad SAS exome
AF:
0.000156
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000165
Gnomad OTH exome
AF:
0.00207
GnomAD4 exome
AF:
0.00207
AC:
2927
AN:
1416404
Hom.:
83
Cov.:
31
AF XY:
0.00173
AC XY:
1210
AN XY:
698446
show subpopulations
Gnomad4 AFR exome
AF:
0.0706
Gnomad4 AMR exome
AF:
0.00490
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000256
Gnomad4 SAS exome
AF:
0.000210
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000103
Gnomad4 OTH exome
AF:
0.00508
GnomAD4 genome
AF:
0.0212
AC:
3230
AN:
152314
Hom.:
112
Cov.:
32
AF XY:
0.0208
AC XY:
1547
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.0727
Gnomad4 AMR
AF:
0.0107
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000221
Gnomad4 OTH
AF:
0.0137
Alfa
AF:
0.000902
Hom.:
1
Bravo
AF:
0.0244
Asia WGS
AF:
0.00404
AC:
14
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJun 29, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.64
Cadd
Benign
2.2
Dann
Benign
0.85

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.037
dbscSNV1_RF
Benign
0.17
SpliceAI score (max)
0.11
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.

Other links and lift over

dbSNP: rs11574669; hg19: chr11-118764298; API