dbSNP rs8031107: IL16:p.Gln469Gln (chr15-81290527-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_172217.5(IL16):c.1407G>A(p.Gln469Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,607,100 control chromosomes in the GnomAD database, including 182,157 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 0.53 ( 22133 hom., cov: 32)

Exomes 𝑓: 0.46 ( 160024 hom. )

Consequence

IL16
NM_172217.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.07

Publications

31 publications found

Variant links:

Genes affected

IL16 (HGNC:5980): (interleukin 16) The protein encoded by this gene is a pleiotropic cytokine that functions as a chemoattractant, a modulator of T cell activation, and an inhibitor of HIV replication. The signaling process of this cytokine is mediated by CD4. The product of this gene undergoes proteolytic processing, which is found to yield two functional proteins. The cytokine function is exclusively attributed to the secreted C-terminal peptide, while the N-terminal product may play a role in cell cycle control. Caspase 3 is reported to be involved in the proteolytic processing of this protein. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]

IL16 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP7

Synonymous conserved (PhyloP=1.07 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL16	NM_172217.5 link	c.1407G>A	p.Gln469Gln	synonymous_variant	Exon 11 of 19	ENST00000683961.1	NP_757366.2	Q14005-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000683961.1 link	c.1407G>A	p.Gln469Gln	synonymous_variant	Exon 11 of 19		NM_172217.5	ENSP00000508085.1		Q14005-1

Frequencies

GnomAD3 genomes

AF:

0.529

AC:

80272

AN:

151830

Hom.:

22077

Cov.:

show subpopulations

Gnomad AFR

AF:

0.686

Gnomad AMI

AF:

0.356

Gnomad AMR

AF:

0.458

Gnomad ASJ

AF:

0.515

Gnomad EAS

AF:

0.537

Gnomad SAS

AF:

0.597

Gnomad FIN

AF:

0.530

Gnomad MID

AF:

0.538

Gnomad NFE

AF:

0.447

Gnomad OTH

AF:

0.516

GnomAD2 exomes

AF:

0.504

AC:

125049

AN:

248208

AF XY:

0.503

show subpopulations

Gnomad AFR exome

AF:

0.690

Gnomad AMR exome

AF:

0.492

Gnomad ASJ exome

AF:

0.494

Gnomad EAS exome

AF:

0.544

Gnomad FIN exome

AF:

0.523

Gnomad NFE exome

AF:

0.451

Gnomad OTH exome

AF:

0.496

GnomAD4 exome

AF:

0.464

AC:

675187

AN:

1455152

Hom.:

160024

Cov.:

AF XY:

0.467

AC XY:

338477

AN XY:

724176

show subpopulations

African (AFR)

AF:

0.699

AC:

23306

AN:

33324

American (AMR)

AF:

0.490

AC:

21808

AN:

44548

Ashkenazi Jewish (ASJ)

AF:

0.498

AC:

12966

AN:

26060

East Asian (EAS)

AF:

0.497

AC:

19695

AN:

39616

South Asian (SAS)

AF:

0.582

AC:

49979

AN:

85802

European-Finnish (FIN)

AF:

0.523

AC:

27902

AN:

53388

Middle Eastern (MID)

AF:

0.531

AC:

3053

AN:

5750

European-Non Finnish (NFE)

AF:

0.440

AC:

487175

AN:

1106514

Other (OTH)

AF:

0.487

AC:

29303

AN:

60150

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

15524

31048

46572

62096

77620

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14882

29764

44646

59528

74410

<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:

0.529

AC:

80393

AN:

151948

Hom.:

22133

Cov.:

AF XY:

0.531

AC XY:

39468

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.686

AC:

28435

AN:

41432

American (AMR)

AF:

0.459

AC:

7007

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.515

AC:

1786

AN:

3468

East Asian (EAS)

AF:

0.537

AC:

2779

AN:

5172

South Asian (SAS)

AF:

0.597

AC:

2874

AN:

4816

European-Finnish (FIN)

AF:

0.530

AC:

5584

AN:

10530

Middle Eastern (MID)

AF:

0.531

AC:

155

AN:

292

European-Non Finnish (NFE)

AF:

0.447

AC:

30348

AN:

67954

Other (OTH)

AF:

0.521

AC:

1101

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1864

3728

5591

7455

9319

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

702

1404

2106

2808

3510

<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:

0.481

Hom.:

56703

Bravo

AF:

0.528

Asia WGS

AF:

0.628

AC:

2186

AN:

3478

EpiCase

AF:

0.450

EpiControl

AF:

0.452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

4.9

(source)

DANN

Benign

0.59

PhyloP100

1.1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over