rs497916

Variant names:

• chr11-118887380-C-T
• rs497916
• NM_001716.5:c.51+3388C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 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]

ENSG00000245869 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCR5	NM_001716.5	MANE Select	c.51+3388C>T		intron	N/A	NP_001707.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCR5	ENST00000292174.5	TSL:1 MANE Select	c.51+3388C>T		intron	N/A	ENSP00000292174.4
	ENSG00000245869	ENST00000498872.2	TSL:1	n.233-126G>A		intron	N/A

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

African (AFR) AF: 0.363 AC: 5721 AN: 15780

American (AMR) AF: 0.328 AC: 323 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 1405 AN: 5156

East Asian (EAS) AF: 0.242 AC: 878 AN: 3630

South Asian (SAS) AF: 0.174 AC: 2859 AN: 16458

European-Finnish (FIN) AF: 0.243 AC: 68 AN: 280

Middle Eastern (MID) AF: 0.240 AC: 389 AN: 1622

European-Non Finnish (NFE) AF: 0.276 AC: 210219 AN: 761858

Other (OTH) AF: 0.270 AC: 7383 AN: 27294

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

African (AFR) AF: 0.358 AC: 14822 AN: 41440

American (AMR) AF: 0.321 AC: 4917 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 945 AN: 3464

East Asian (EAS) AF: 0.224 AC: 1162 AN: 5180

South Asian (SAS) AF: 0.167 AC: 803 AN: 4822

European-Finnish (FIN) AF: 0.288 AC: 3036 AN: 10552

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.284 AC: 19330 AN: 67972

Other (OTH) AF: 0.287 AC: 607 AN: 2114

Alfa AF: 0.289 Hom.: 11037

Bravo AF: 0.312

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.6
DANN	Benign	0.48
PhyloP100		-0.65
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: rs497916; hg19: chr11-118758089; COSMIC: COSV52690090;