NM_001716.5:c.*316C>G

Variant names:

• chr11-118894979-C-G
• rs676925
• NM_001716.5:c.*316C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001716.5(CXCR5):​c.*316C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 300,020 control chromosomes in the GnomAD database, including 8,263 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 0.20 (4160 hom., cov: 32)
  • Exomes 𝑓: 0.22 (4103 hom.)
• Consequence: CXCR5 NM_001716.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 19 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]

BCL9L (HGNC:23688): (BCL9 like) Enables beta-catenin binding activity. Involved in several processes, including negative regulation of transforming growth factor beta receptor signaling pathway; positive regulation of epithelial to mesenchymal transition; and positive regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Apr 2022]

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 (AMR) allele frequency at 95% confidence interval = 0.365 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCR5	NM_001716.5	MANE Select	c.*316C>G		3_prime_UTR	Exon 2 of 2	NP_001707.1	P32302-1
	CXCR5	NM_032966.2		c.*316C>G		3_prime_UTR	Exon 1 of 1	NP_116743.1	P32302-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCR5	ENST00000292174.5	TSL:1 MANE Select	c.*316C>G		3_prime_UTR	Exon 2 of 2	ENSP00000292174.4	P32302-1
	BCL9L	ENST00000334801.7	TSL:1	c.*3436G>C		3_prime_UTR	Exon 8 of 8	ENSP00000335320.3	Q86UU0-1

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31109 AN: 152022 Hom.: 4147 Cov.: 32

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.211

GnomAD4 exome AF: 0.221 AC: 32618 AN: 147880 Hom.: 4103 Cov.: 0 AF XY: 0.221 AC XY: 16344 AN XY: 73940

African (AFR) AF: 0.0627 AC: 291 AN: 4644

American (AMR) AF: 0.382 AC: 1732 AN: 4534

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 1060 AN: 5458

East Asian (EAS) AF: 0.0541 AC: 634 AN: 11728

South Asian (SAS) AF: 0.133 AC: 214 AN: 1608

European-Finnish (FIN) AF: 0.250 AC: 6010 AN: 24014

Middle Eastern (MID) AF: 0.172 AC: 124 AN: 720

European-Non Finnish (NFE) AF: 0.238 AC: 20479 AN: 85936

Other (OTH) AF: 0.225 AC: 2074 AN: 9238

GnomAD4 genome AF: 0.205 AC: 31135 AN: 152140 Hom.: 4160 Cov.: 32 AF XY: 0.207 AC XY: 15386 AN XY: 74386

African (AFR) AF: 0.0622 AC: 2583 AN: 41532

American (AMR) AF: 0.373 AC: 5702 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 713 AN: 3470

East Asian (EAS) AF: 0.106 AC: 550 AN: 5168

South Asian (SAS) AF: 0.144 AC: 696 AN: 4828

European-Finnish (FIN) AF: 0.259 AC: 2739 AN: 10578

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17433 AN: 67972

Other (OTH) AF: 0.209 AC: 442 AN: 2112

Alfa AF: 0.229 Hom.: 661

Bravo AF: 0.208

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.54
PhyloP100		0.074
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: rs676925; hg19: chr11-118765688; COSMIC: COSV52690465; COSMIC: COSV52690465;