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GeneBe

11-118894372-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001716.5(CXCR5):c.828C>T(p.His276=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00167 in 1,614,202 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0086 ( 13 hom., cov: 32)
Exomes 𝑓: 0.00095 ( 15 hom. )

Consequence

CXCR5
NM_001716.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0440
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]
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
Variant 11-118894372-C-T is Benign according to our data. Variant chr11-118894372-C-T is described in ClinVar as [Benign]. Clinvar id is 784217.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.044 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00863 (1314/152332) while in subpopulation AFR AF= 0.0298 (1237/41568). AF 95% confidence interval is 0.0284. There are 13 homozygotes in gnomad4. There are 601 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
High AC in GnomAd at 1307 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CXCR5NM_001716.5 linkuse as main transcriptc.828C>T p.His276= synonymous_variant 2/2 ENST00000292174.5
CXCR5NM_032966.2 linkuse as main transcriptc.693C>T p.His231= synonymous_variant 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CXCR5ENST00000292174.5 linkuse as main transcriptc.828C>T p.His276= synonymous_variant 2/21 NM_001716.5 P1P32302-1
BCL9LENST00000334801.7 linkuse as main transcriptc.*4043G>A 3_prime_UTR_variant 8/81 P4Q86UU0-1

Frequencies

GnomAD3 genomes
AF:
0.00859
AC:
1307
AN:
152214
Hom.:
13
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0297
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00288
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.00956
GnomAD3 exomes
AF:
0.00214
AC:
538
AN:
251020
Hom.:
1
AF XY:
0.00144
AC XY:
196
AN XY:
135698
show subpopulations
Gnomad AFR exome
AF:
0.0292
Gnomad AMR exome
AF:
0.00142
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000971
Gnomad OTH exome
AF:
0.000489
GnomAD4 exome
AF:
0.000948
AC:
1386
AN:
1461870
Hom.:
15
Cov.:
31
AF XY:
0.000777
AC XY:
565
AN XY:
727240
show subpopulations
Gnomad4 AFR exome
AF:
0.0309
Gnomad4 AMR exome
AF:
0.00170
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000348
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000126
Gnomad4 OTH exome
AF:
0.00207
GnomAD4 genome
AF:
0.00863
AC:
1314
AN:
152332
Hom.:
13
Cov.:
32
AF XY:
0.00807
AC XY:
601
AN XY:
74494
show subpopulations
Gnomad4 AFR
AF:
0.0298
Gnomad4 AMR
AF:
0.00287
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.00946
Alfa
AF:
0.00420
Hom.:
4
Bravo
AF:
0.00957
Asia WGS
AF:
0.00260
AC:
9
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.000178

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
-0.63
Cadd
Benign
3.1
Dann
Benign
0.85

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.

Other links and lift over

dbSNP: rs2230320; hg19: chr11-118765081; API