rs1790192

Variant names:

• chr11-118886482-G-A
• rs1790192
• NM_001716.5:c.51+2490G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-118886482-G-A
• chr11-118886482-G-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate 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
• Publications: 13 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.127).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.592 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.51+2490G>A		intron	N/A	NP_001707.1	P32302-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCR5	ENST00000292174.5	TSL:1 MANE Select	c.51+2490G>A		intron	N/A	ENSP00000292174.4	P32302-1
	ENSG00000245869	ENST00000498872.2	TSL:1	n.1005C>T		non_coding_transcript_exon	Exon 2 of 2

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

GnomAD2 exomes AF: 0.582 AC: 44793 AN: 76978 AF XY: 0.588

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 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

African (AFR) AF: 0.537 AC: 2995 AN: 5574

American (AMR) AF: 0.393 AC: 5005 AN: 12728

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 4594 AN: 7232

East Asian (EAS) AF: 0.572 AC: 4705 AN: 8224

South Asian (SAS) AF: 0.550 AC: 26750 AN: 48662

European-Finnish (FIN) AF: 0.613 AC: 6039 AN: 9846

Middle Eastern (MID) AF: 0.656 AC: 1513 AN: 2308

European-Non Finnish (NFE) AF: 0.627 AC: 83695 AN: 133508

Other (OTH) AF: 0.610 AC: 6873 AN: 11264

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

African (AFR) AF: 0.534 AC: 21994 AN: 41192

American (AMR) AF: 0.426 AC: 6453 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2005 AN: 3458

East Asian (EAS) AF: 0.564 AC: 2897 AN: 5136

South Asian (SAS) AF: 0.503 AC: 2403 AN: 4776

European-Finnish (FIN) AF: 0.583 AC: 6094 AN: 10444

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40498 AN: 67824

Other (OTH) AF: 0.584 AC: 1221 AN: 2092

Alfa AF: 0.569 Hom.: 6001

Bravo AF: 0.541

Asia WGS AF: 0.504 AC: 1754 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.40
PhyloP100		0.36
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: rs1790192; hg19: chr11-118757191;