Genetic Variant CXCL9:c.*1763T>C (chr4-76001835-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002416.3(CXCL9):c.*1763T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 161,956 control chromosomes in the GnomAD database, including 32,246 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 0.62 ( 30669 hom., cov: 31)

Exomes 𝑓: 0.55 ( 1577 hom. )

Consequence

CXCL9
NM_002416.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.481

Publications

49 publications found

Variant links:

Genes affected

CXCL9 (HGNC:7098): (C-X-C motif chemokine ligand 9) This antimicrobial gene is part of a chemokine superfamily that encodes secreted proteins involved in immunoregulatory and inflammatory processes. The protein encoded is thought to be involved in T cell trafficking. The encoded protein binds to C-X-C motif chemokine 3 and is a chemoattractant for lymphocytes but not for neutrophils. [provided by RefSeq, Aug 2020]

CXCL9 links:

SDAD1-AS1 (HGNC:41106): (SDAD1 antisense RNA 1)

SDAD1-AS1 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CXCL9	NM_002416.3 link	c.*1763T>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000264888.6	NP_002407.1	Q07325
SDAD1-AS1	NR_125906.1 link	n.816-3238A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CXCL9	ENST00000264888.6 link	c.*1763T>C		3_prime_UTR_variant	Exon 4 of 4	1	NM_002416.3	ENSP00000354901.4		Q07325
SDAD1-AS1	ENST00000501239.2 link	n.816-3238A>G		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes

AF:

0.623

AC:

94591

AN:

151866

Hom.:

30609

Cov.:

show subpopulations

Gnomad AFR

AF:

0.732

Gnomad AMI

AF:

0.670

Gnomad AMR

AF:

0.725

Gnomad ASJ

AF:

0.595

Gnomad EAS

AF:

0.939

Gnomad SAS

AF:

0.548

Gnomad FIN

AF:

0.481

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.538

Gnomad OTH

AF:

0.630

GnomAD4 exome

AF:

0.549

AC:

5476

AN:

9972

Hom.:

1577

Cov.:

AF XY:

0.552

AC XY:

2875

AN XY:

5210

show subpopulations

African (AFR)

AF:

0.729

AC:

293

AN:

402

American (AMR)

AF:

0.752

AC:

212

AN:

282

Ashkenazi Jewish (ASJ)

AF:

0.605

AC:

270

AN:

446

East Asian (EAS)

AF:

0.904

AC:

629

AN:

696

South Asian (SAS)

AF:

0.472

AC:

AN:

European-Finnish (FIN)

AF:

0.459

AC:

361

AN:

786

Middle Eastern (MID)

AF:

0.675

AC:

AN:

European-Non Finnish (NFE)

AF:

0.497

AC:

3308

AN:

6656

Other (OTH)

AF:

0.578

AC:

342

AN:

592

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

117

233

350

466

583

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.623

AC:

94719

AN:

151984

Hom.:

30669

Cov.:

AF XY:

0.622

AC XY:

46225

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.733

AC:

30360

AN:

41426

American (AMR)

AF:

0.725

AC:

11079

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.595

AC:

2063

AN:

3468

East Asian (EAS)

AF:

0.939

AC:

4862

AN:

5176

South Asian (SAS)

AF:

0.549

AC:

2636

AN:

4802

European-Finnish (FIN)

AF:

0.481

AC:

5081

AN:

10572

Middle Eastern (MID)

AF:

0.592

AC:

174

AN:

294

European-Non Finnish (NFE)

AF:

0.538

AC:

36526

AN:

67950

Other (OTH)

AF:

0.630

AC:

1327

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1713

3426

5140

6853

8566

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.578

Hom.:

35879

Bravo

AF:

0.652

Asia WGS

AF:

0.725

AC:

2517

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.67

(source)

DANN

Benign

0.31

PhyloP100

-0.48

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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4-76001835-A-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over