rs566416

Variant names:

• chr11-118888901-T-G
• rs566416
• NM_001716.5:c.52-4695T>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.52-4695T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,120 control chromosomes in the GnomAD database, including 3,713 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 0.19 (3713 hom., cov: 32)
• Consequence: CXCR5 NM_001716.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 23 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CXCR5	NM_001716.5	c.52-4695T>G		intron_variant	Intron 1 of 1	ENST00000292174.5	NP_001707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CXCR5	ENST00000292174.5	c.52-4695T>G		intron_variant	Intron 1 of 1	1	NM_001716.5	ENSP00000292174.4

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28871 AN: 152002 Hom.: 3700 Cov.: 32

Gnomad AFR AF: 0.0483

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0962

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.201

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.190 AC: 28890 AN: 152120 Hom.: 3713 Cov.: 32 AF XY: 0.191 AC XY: 14179 AN XY: 74370

African (AFR) AF: 0.0481 AC: 1998 AN: 41524

American (AMR) AF: 0.364 AC: 5568 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3466

East Asian (EAS) AF: 0.0966 AC: 500 AN: 5174

South Asian (SAS) AF: 0.133 AC: 643 AN: 4828

European-Finnish (FIN) AF: 0.214 AC: 2265 AN: 10580

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.243 AC: 16544 AN: 67958

Other (OTH) AF: 0.199 AC: 420 AN: 2114

Alfa AF: 0.228 Hom.: 10469

Bravo AF: 0.196

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.52
PhyloP100		-1.2
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: rs566416; hg19: chr11-118759610;