11-118886482-G-A

Position:

• chr11-118886482-G-A

Variant summary

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

The NM_001716.5(CXCR5):​c.51+2490G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,272 control chromosomes in the GnomAD database, including 23,874 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 0.56 (23874 hom., cov: 29)
  • Exomes 𝑓: 0.59 (45922 hom.)
  • Failed GnomAD Quality Control
• Consequence: CXCR5 NM_001716.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CXCR5	NM_001716.5	c.51+2490G>A		intron_variant		ENST00000292174.5	NP_001707.1
LOC124902767	XR_007062913.1	n.1526C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CXCR5	ENST00000292174.5	c.51+2490G>A		intron_variant		1	NM_001716.5	ENSP00000292174	P1
	ENST00000498872.2	n.1005C>T		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84225 AN: 151154 Hom.: 23883 Cov.: 29

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.585

GnomAD3 exomes AF: 0.582 AC: 44793 AN: 76978 Hom.: 14600 AF XY: 0.588 AC XY: 25244 AN XY: 42936

Gnomad AFR exome AF: 0.543

Gnomad AMR exome AF: 0.405

Gnomad ASJ exome AF: 0.659

Gnomad EAS exome AF: 0.575

Gnomad SAS exome AF: 0.563

Gnomad FIN exome AF: 0.651

Gnomad NFE exome AF: 0.644

Gnomad OTH exome AF: 0.609

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.594 AC: 142169 AN: 239346 Hom.: 45922 Cov.: 0 AF XY: 0.592 AC XY: 81639 AN XY: 137974

Gnomad4 AFR exome AF: 0.537

Gnomad4 AMR exome AF: 0.393

Gnomad4 ASJ exome AF: 0.635

Gnomad4 EAS exome AF: 0.572

Gnomad4 SAS exome AF: 0.550

Gnomad4 FIN exome AF: 0.613

Gnomad4 NFE exome AF: 0.627

Gnomad4 OTH exome AF: 0.610

GnomAD4 genome AF: 0.557 AC: 84231 AN: 151272 Hom.: 23874 Cov.: 29 AF XY: 0.553 AC XY: 40850 AN XY: 73872

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.584

Alfa AF: 0.592 Hom.: 3864

Bravo AF: 0.541

Asia WGS AF: 0.504 AC: 1754 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.40

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: rs1790192; hg19: chr11-118757191;