rs78440425

Variant names:

• chr11-118888302-G-A
• rs78440425
• NM_001716.5:c.51+4310G>A

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+4310G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 152,156 control chromosomes in the GnomAD database, including 52 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 0.012 (52 hom., cov: 32)
• Consequence: CXCR5 NM_001716.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 8 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]

LOC124902767 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CXCR5	NM_001716.5	c.51+4310G>A		intron_variant	Intron 1 of 1	ENST00000292174.5	NP_001707.1
LOC124902767	XR_007062913.1	n.-199C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CXCR5	ENST00000292174.5	c.51+4310G>A		intron_variant	Intron 1 of 1	1	NM_001716.5	ENSP00000292174.4

Frequencies

GnomAD3 genomes AF: 0.0124 AC: 1884 AN: 152038 Hom.: 52 Cov.: 32

Gnomad AFR AF: 0.00225

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00603

Gnomad ASJ AF: 0.00547

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0464

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00735

Gnomad OTH AF: 0.00910

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0124 AC: 1881 AN: 152156 Hom.: 52 Cov.: 32 AF XY: 0.0145 AC XY: 1082 AN XY: 74372

African (AFR) AF: 0.00224 AC: 93 AN: 41498

American (AMR) AF: 0.00602 AC: 92 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00547 AC: 19 AN: 3472

East Asian (EAS) AF: 0.113 AC: 582 AN: 5172

South Asian (SAS) AF: 0.0172 AC: 83 AN: 4814

European-Finnish (FIN) AF: 0.0464 AC: 492 AN: 10598

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.00735 AC: 500 AN: 68004

Other (OTH) AF: 0.00900 AC: 19 AN: 2110

Alfa AF: 0.00815 Hom.: 3

Bravo AF: 0.00931

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.4
DANN	Benign	0.67
PhyloP100		0.31
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: rs78440425; hg19: chr11-118759011;