rs566416

Positions:

• chr11-118888901-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CXCR5	NM_001716.5	c.52-4695T>G		intron_variant		ENST00000292174.5	NP_001707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CXCR5	ENST00000292174.5	c.52-4695T>G		intron_variant		1	NM_001716.5	ENSP00000292174	P1

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

Gnomad4 AFR AF: 0.0481

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.0966

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.199

Alfa AF: 0.231 Hom.: 6723

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

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

Other links and lift over

dbSNP: rs566416; hg19: chr11-118759610;