Genetic Variant NM_001386809.1:c.-153G>T (chr17-4739492-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001386809.1(CXCL16):c.-153G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 1,125,220 control chromosomes in the GnomAD database, including 171,660 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 ( 23637 hom., cov: 34)

Exomes 𝑓: 0.55 ( 148023 hom. )

Consequence

CXCL16
NM_001386809.1 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.53

Publications

7 publications found

Variant links:

Genes affected

CXCL16 (HGNC:16642): (C-X-C motif chemokine ligand 16) Enables chemokine activity. Involved in several processes, including positive regulation of cell growth; response to interferon-gamma; and response to tumor necrosis factor. Located in extracellular space. Biomarker of COVID-19 and systemic scleroderma. [provided by Alliance of Genome Resources, Apr 2022]

CXCL16 links:

Genome browser will be placed here

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=-0.77).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CXCL16	NM_001386809.1 link	c.-153G>T		5_prime_UTR_variant	Exon 1 of 6	ENST00000293778.12	NP_001373738.1
CXCL16	NM_001100812.2 link	c.-153G>T		5_prime_UTR_variant	Exon 1 of 5		NP_001094282.2	Q9H2A7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CXCL16	ENST00000293778.12 link	c.-153G>T		5_prime_UTR_variant	Exon 1 of 6	1	NM_001386809.1	ENSP00000293778.7		Q9H2A7
CXCL16	ENST00000574412.6 link	c.-153G>T		5_prime_UTR_variant	Exon 1 of 5	1		ENSP00000459592.2		Q9H2A7

Frequencies

GnomAD3 genomes

AF:

0.556

AC:

84551

AN:

151946

Hom.:

23612

Cov.:

show subpopulations

Gnomad AFR

AF:

0.557

Gnomad AMI

AF:

0.414

Gnomad AMR

AF:

0.621

Gnomad ASJ

AF:

0.619

Gnomad EAS

AF:

0.600

Gnomad SAS

AF:

0.589

Gnomad FIN

AF:

0.520

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.539

Gnomad OTH

AF:

0.590

GnomAD4 exome

AF:

0.548

AC:

533334

AN:

973156

Hom.:

148023

Cov.:

AF XY:

0.551

AC XY:

273685

AN XY:

496866

show subpopulations

African (AFR)

AF:

0.557

AC:

12754

AN:

22892

American (AMR)

AF:

0.614

AC:

18763

AN:

30536

Ashkenazi Jewish (ASJ)

AF:

0.611

AC:

13029

AN:

21318

East Asian (EAS)

AF:

0.578

AC:

19669

AN:

34026

South Asian (SAS)

AF:

0.596

AC:

42094

AN:

70676

European-Finnish (FIN)

AF:

0.525

AC:

18298

AN:

34878

Middle Eastern (MID)

AF:

0.569

AC:

1796

AN:

3156

European-Non Finnish (NFE)

AF:

0.537

AC:

382503

AN:

711896

Other (OTH)

AF:

0.558

AC:

24428

AN:

43778

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

12622

25244

37865

50487

63109

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9062

18124

27186

36248

45310

<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:

0.557

AC:

84633

AN:

152064

Hom.:

23637

Cov.:

AF XY:

0.558

AC XY:

41507

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.557

AC:

23116

AN:

41512

American (AMR)

AF:

0.621

AC:

9488

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.619

AC:

2145

AN:

3464

East Asian (EAS)

AF:

0.601

AC:

3078

AN:

5120

South Asian (SAS)

AF:

0.590

AC:

2842

AN:

4820

European-Finnish (FIN)

AF:

0.520

AC:

5517

AN:

10600

Middle Eastern (MID)

AF:

0.609

AC:

179

AN:

294

European-Non Finnish (NFE)

AF:

0.539

AC:

36645

AN:

67944

Other (OTH)

AF:

0.590

AC:

1245

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1955

3910

5866

7821

9776

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

732

1464

2196

2928

3660

<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:

0.467

Hom.:

1888

Bravo

AF:

0.564

Asia WGS

AF:

0.616

AC:

2144

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

3.3

(source)

DANN

Benign

0.74

PhyloP100

-1.5

PromoterAI

-0.0038

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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