Variant rs6817952 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000306621.8(CXCL11):c.61+37C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,562,256 control chromosomes in the GnomAD database, including 19,468 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 0.13 ( 1684 hom., cov: 33)

Exomes 𝑓: 0.15 ( 17784 hom. )

Consequence

CXCL11
ENST00000306621.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.140

Variant links:

Genes affected

CXCL11 (HGNC:10638): (C-X-C motif chemokine ligand 11) Chemokines are a group of small (approximately 8 to 14 kD), mostly basic, structurally related molecules that regulate cell trafficking of various types of leukocytes through interactions with a subset of 7-transmembrane, G protein-coupled receptors. Chemokines also play fundamental roles in the development, homeostasis, and function of the immune system, and they have effects on cells of the central nervous system as well as on endothelial cells involved in angiogenesis or angiostasis. Chemokines are divided into 2 major subfamilies, CXC and CC. This antimicrobial gene is a CXC member of the chemokine superfamily. Its encoded protein induces a chemotactic response in activated T-cells and is the dominant ligand for CXC receptor-3. The gene encoding this protein contains 4 exons and at least three polyadenylation signals which might reflect cell-specific regulation of expression. IFN-gamma is a potent inducer of transcription of this gene. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2014]

CXCL11 links:

ART3 (HGNC:725): (ADP-ribosyltransferase 3 (inactive)) This gene encodes an arginine-specific ADP-ribosyltransferase. The encoded protein catalyzes a reversible reaction which modifies proteins by the addition or removal of ADP-ribose to an arginine residue to regulate the function of the modified protein. An ADP-ribosyltransferase pseudogene is located on chromosome 11. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ART3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CXCL11	NM_005409.5 linkuse as main transcript	c.61+37C>T		intron_variant		ENST00000306621.8	NP_005400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CXCL11	ENST00000306621.8 linkuse as main transcript	c.61+37C>T		intron_variant		1	NM_005409.5	ENSP00000306884	P1

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19708

AN:

152082

Hom.:

1682

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0564

Gnomad AMI

AF:

0.248

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.189

Gnomad EAS

AF:

0.386

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.149

Gnomad OTH

AF:

0.123

GnomAD3 exomes

AF:

0.155

AC:

36418

AN:

234948

Hom.:

3595

AF XY:

0.153

AC XY:

19457

AN XY:

126956

show subpopulations

Gnomad AFR exome

AF:

0.0536

Gnomad AMR exome

AF:

0.169

Gnomad ASJ exome

AF:

0.183

Gnomad EAS exome

AF:

0.393

Gnomad SAS exome

AF:

0.103

Gnomad FIN exome

AF:

0.0988

Gnomad NFE exome

AF:

0.149

Gnomad OTH exome

AF:

0.154

GnomAD4 exome

AF:

0.151

AC:

213112

AN:

1410056

Hom.:

17784

Cov.:

AF XY:

0.151

AC XY:

105839

AN XY:

703170

show subpopulations

Gnomad4 AFR exome

AF:

0.0498

Gnomad4 AMR exome

AF:

0.165

Gnomad4 ASJ exome

AF:

0.185

Gnomad4 EAS exome

AF:

0.375

Gnomad4 SAS exome

AF:

0.102

Gnomad4 FIN exome

AF:

0.0995

Gnomad4 NFE exome

AF:

0.151

Gnomad4 OTH exome

AF:

0.152

GnomAD4 genome

AF:

0.130

AC:

19715

AN:

152200

Hom.:

1684

Cov.:

AF XY:

0.129

AC XY:

9580

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0563

Gnomad4 AMR

AF:

0.151

Gnomad4 ASJ

AF:

0.189

Gnomad4 EAS

AF:

0.386

Gnomad4 SAS

AF:

0.124

Gnomad4 FIN

AF:

0.106

Gnomad4 NFE

AF:

0.149

Gnomad4 OTH

AF:

0.125

Alfa

AF:

0.138

Hom.:

309

Bravo

AF:

0.131

Asia WGS

AF:

0.240

AC:

831

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

9.6

DANN

Benign

0.69

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over