11-118893342-C-T

Position:

• chr11-118893342-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001716.5(CXCR5):​c.52-254C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 972,114 control chromosomes in the GnomAD database, including 38,143 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 0.33 (9035 hom., cov: 32)
  • Exomes 𝑓: 0.26 (29108 hom.)
• Consequence: CXCR5 NM_001716.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710

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 (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CXCR5	NM_001716.5	c.52-254C>T		intron_variant		ENST00000292174.5	NP_001707.1
CXCR5	NM_032966.2	c.-338C>T		upstream_gene_variant			NP_116743.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CXCR5	ENST00000292174.5	c.52-254C>T		intron_variant		1	NM_001716.5	ENSP00000292174.4

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50386 AN: 151938 Hom.: 8996 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.309

GnomAD4 exome AF: 0.263 AC: 215818 AN: 820058 Hom.: 29108 Cov.: 15 AF XY: 0.263 AC XY: 99557 AN XY: 379204

Gnomad4 AFR exome AF: 0.446

Gnomad4 AMR exome AF: 0.443

Gnomad4 ASJ exome AF: 0.235

Gnomad4 EAS exome AF: 0.230

Gnomad4 SAS exome AF: 0.176

Gnomad4 FIN exome AF: 0.255

Gnomad4 NFE exome AF: 0.262

Gnomad4 OTH exome AF: 0.260

GnomAD4 genome AF: 0.332 AC: 50474 AN: 152056 Hom.: 9035 Cov.: 32 AF XY: 0.335 AC XY: 24866 AN XY: 74310

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.306

Alfa AF: 0.315 Hom.: 3101

Bravo AF: 0.347

Asia WGS AF: 0.180 AC: 627 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	0.98
DANN	Benign	0.54

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: rs613791; hg19: chr11-118764051;