rs497916

Positions:

• chr11-118887380-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.51+3388C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 985,098 control chromosomes in the GnomAD database, including 38,936 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 0.30 (7154 hom., cov: 31)
  • Exomes 𝑓: 0.28 (31782 hom.)
• Consequence: CXCR5 NM_001716.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648

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]

LOC124902767 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CXCR5	NM_001716.5	c.51+3388C>T		intron_variant		ENST00000292174.5
LOC124902767	XR_007062913.1	n.724G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CXCR5	ENST00000292174.5	c.51+3388C>T		intron_variant		1	NM_001716.5	P1
	ENST00000498872.2	n.233-126G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45849 AN: 151918 Hom.: 7126 Cov.: 31

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.289

GnomAD4 exome AF: 0.275 AC: 229245 AN: 833062 Hom.: 31782 Cov.: 30 AF XY: 0.274 AC XY: 105519 AN XY: 384686

Gnomad4 AFR exome AF: 0.363

Gnomad4 AMR exome AF: 0.328

Gnomad4 ASJ exome AF: 0.272

Gnomad4 EAS exome AF: 0.242

Gnomad4 SAS exome AF: 0.174

Gnomad4 FIN exome AF: 0.243

Gnomad4 NFE exome AF: 0.276

Gnomad4 OTH exome AF: 0.270

GnomAD4 genome AF: 0.302 AC: 45926 AN: 152036 Hom.: 7154 Cov.: 31 AF XY: 0.299 AC XY: 22191 AN XY: 74336

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.287

Alfa AF: 0.285 Hom.: 8496

Bravo AF: 0.312

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.6
DANN	Benign	0.48

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: rs497916; hg19: chr11-118758089; COSMIC: COSV52690090;