11-118894891-A-G

Variant names:

• chr11-118894891-A-G
• rs3922
• NM_001716.5:c.*228A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001716.5(CXCR5):​c.*228A>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 0.431 in 454,224 control chromosomes in the GnomAD database, including 44,753 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 0.48 (18682 hom., cov: 32)
  • Exomes 𝑓: 0.41 (26071 hom.)
• Consequence: CXCR5 NM_001716.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 44 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 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.*228A>G		3_prime_UTR	Exon 2 of 2	NP_001707.1	P32302-1
	CXCR5	NM_032966.2		c.*228A>G		3_prime_UTR	Exon 1 of 1	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.*228A>G		3_prime_UTR	Exon 2 of 2	ENSP00000292174.4	P32302-1
	BCL9L	ENST00000334801.7	TSL:1	c.*3524T>C		3_prime_UTR	Exon 8 of 8	ENSP00000335320.3	Q86UU0-1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73290 AN: 151886 Hom.: 18632 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.472

GnomAD4 exome AF: 0.405 AC: 122544 AN: 302220 Hom.: 26071 Cov.: 4 AF XY: 0.404 AC XY: 61932 AN XY: 153134

African (AFR) AF: 0.624 AC: 5378 AN: 8624

American (AMR) AF: 0.560 AC: 6075 AN: 10844

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 4353 AN: 9910

East Asian (EAS) AF: 0.225 AC: 5689 AN: 25238

South Asian (SAS) AF: 0.251 AC: 1955 AN: 7800

European-Finnish (FIN) AF: 0.424 AC: 15234 AN: 35920

Middle Eastern (MID) AF: 0.457 AC: 635 AN: 1390

European-Non Finnish (NFE) AF: 0.408 AC: 75183 AN: 184292

Other (OTH) AF: 0.442 AC: 8042 AN: 18202

GnomAD4 genome AF: 0.483 AC: 73386 AN: 152004 Hom.: 18682 Cov.: 32 AF XY: 0.482 AC XY: 35771 AN XY: 74282

African (AFR) AF: 0.636 AC: 26381 AN: 41460

American (AMR) AF: 0.547 AC: 8363 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1533 AN: 3468

East Asian (EAS) AF: 0.303 AC: 1562 AN: 5158

South Asian (SAS) AF: 0.253 AC: 1219 AN: 4824

European-Finnish (FIN) AF: 0.436 AC: 4604 AN: 10570

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28275 AN: 67922

Other (OTH) AF: 0.468 AC: 990 AN: 2114

Alfa AF: 0.436 Hom.: 68128

Bravo AF: 0.501

Asia WGS AF: 0.288 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.027
DANN	Benign	0.24
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3922; hg19: chr11-118765600; COSMIC: COSV52685125; COSMIC: COSV52685125;