Genetic Variant NM_002416.3: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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002416.3. 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
	CXCL9	NM_002416.3	MANE Select	c.*1763T>C		3_prime_UTR	Exon 4 of 4	NP_002407.1	Q07325
	SDAD1-AS1	NR_125906.1		n.816-3238A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCL9	ENST00000264888.6	TSL:1 MANE Select	c.*1763T>C		3_prime_UTR	Exon 4 of 4	ENSP00000354901.4	Q07325
	SDAD1-AS1	ENST00000501239.2	TSL:1	n.816-3238A>G		intron	N/A

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

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

Age Distribution

Genome Het

Genome Hom

Variant carriers

760

1520

2280

3040

3800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over