rs2280964

Variant names:

• chrX-71618204-C-A
• rs2280964
• NM_001504.2:c.12+234G>T

Your query was ambiguous. Multiple possible variants found:

• chrX-71618204-C-A
• chrX-71618204-C-G
• chrX-71618204-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001504.2(CXCR3):​c.12+234G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.000019 (0 hom., 1 hem., cov: 19)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: CXCR3 NM_001504.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 26 publications found

Genes affected

CXCR3 (HGNC:4540): (C-X-C motif chemokine receptor 3) This gene encodes a G protein-coupled receptor with selectivity for three chemokines, termed CXCL9/Mig (monokine induced by interferon-g), CXCL10/IP10 (interferon-g-inducible 10 kDa protein) and CXCL11/I-TAC (interferon-inducible T cell a-chemoattractant). Binding of chemokines to this protein induces cellular responses that are involved in leukocyte traffic, most notably integrin activation, cytoskeletal changes and chemotactic migration. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. One of the isoforms (CXCR3-B) shows high affinity binding to chemokine, CXCL4/PF4 (PMID:12782716). [provided by RefSeq, Jun 2011]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001504.2. 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
	CXCR3	NM_001504.2	MANE Select	c.12+234G>T		intron	N/A	NP_001495.1
	CXCR3	NM_001142797.2		c.-92+234G>T		intron	N/A	NP_001136269.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCR3	ENST00000373693.4	TSL:1 MANE Select	c.12+234G>T		intron	N/A	ENSP00000362797.3
	CXCR3	ENST00000373691.4	TSL:1	c.-92+234G>T		intron	N/A	ENSP00000362795.4

Frequencies

GnomAD3 genomes AF: 0.0000193 AC: 2 AN: 103359 Hom.: 0 Cov.: 19

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000397

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 5474 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 1004

African (AFR) AF: 0.00 AC: 0 AN: 93

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 49

East Asian (EAS) AF: 0.00 AC: 0 AN: 25

South Asian (SAS) AF: 0.00 AC: 0 AN: 105

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 5000

Other (OTH) AF: 0.00 AC: 0 AN: 190

GnomAD4 genome AF: 0.0000193 AC: 2 AN: 103359 Hom.: 0 Cov.: 19 AF XY: 0.0000376 AC XY: 1 AN XY: 26621

African (AFR) AF: 0.00 AC: 0 AN: 27942

American (AMR) AF: 0.00 AC: 0 AN: 9747

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2488

East Asian (EAS) AF: 0.00 AC: 0 AN: 3176

South Asian (SAS) AF: 0.00 AC: 0 AN: 2085

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5336

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 232

European-Non Finnish (NFE) AF: 0.0000397 AC: 2 AN: 50356

Other (OTH) AF: 0.00 AC: 0 AN: 1364

Alfa AF: 0.00 Hom.: 15915

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.93
DANN	Benign	0.42
PhyloP100		-0.18
PromoterAI		0.040	Neutral

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: rs2280964; hg19: chrX-70838054;