dbSNP rs4778636: IL16:c.2054-82G>A (chr15-81299298-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_172217.5(IL16):c.2054-82G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0952 in 1,598,460 control chromosomes in the GnomAD database, including 8,664 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 0.12 ( 1555 hom., cov: 33)

Exomes 𝑓: 0.092 ( 7109 hom. )

Consequence

IL16
NM_172217.5 intron

Scores

Splicing: ADA: 0.00001420

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.95

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL16	NM_172217.5 link	c.2054-82G>A		intron_variant	Intron 13 of 18	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.2054-82G>A		intron_variant	Intron 13 of 18		NM_172217.5	ENSP00000508085.1		Q14005-1

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18821

AN:

152060

Hom.:

1548

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.0714

Gnomad AMR

AF:

0.131

Gnomad ASJ

AF:

0.0536

Gnomad EAS

AF:

0.176

Gnomad SAS

AF:

0.0600

Gnomad FIN

AF:

0.0303

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0781

Gnomad OTH

AF:

0.116

GnomAD3 exomes

AF:

0.100

AC:

23698

AN:

236642

Hom.:

1528

AF XY:

0.0925

AC XY:

11961

AN XY:

129336

show subpopulations

Gnomad AFR exome

AF:

0.228

Gnomad AMR exome

AF:

0.139

Gnomad ASJ exome

AF:

0.0540

Gnomad EAS exome

AF:

0.183

Gnomad SAS exome

AF:

0.0519

Gnomad FIN exome

AF:

0.0394

Gnomad NFE exome

AF:

0.0814

Gnomad OTH exome

AF:

0.0899

GnomAD4 exome

AF:

0.0921

AC:

133259

AN:

1446282

Hom.:

7109

Cov.:

AF XY:

0.0897

AC XY:

64589

AN XY:

719926

show subpopulations

Gnomad4 AFR exome

AF:

0.234

Gnomad4 AMR exome

AF:

0.141

Gnomad4 ASJ exome

AF:

0.0537

Gnomad4 EAS exome

AF:

0.181

Gnomad4 SAS exome

AF:

0.0537

Gnomad4 FIN exome

AF:

0.0453

Gnomad4 NFE exome

AF:

0.0883

Gnomad4 OTH exome

AF:

0.0960

GnomAD4 genome

AF:

0.124

AC:

18848

AN:

152178

Hom.:

1555

Cov.:

AF XY:

0.119

AC XY:

8878

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.229

Gnomad4 AMR

AF:

0.130

Gnomad4 ASJ

AF:

0.0536

Gnomad4 EAS

AF:

0.176

Gnomad4 SAS

AF:

0.0599

Gnomad4 FIN

AF:

0.0303

Gnomad4 NFE

AF:

0.0781

Gnomad4 OTH

AF:

0.114

Alfa

AF:

0.0879

Hom.:

1007

Bravo

AF:

0.139

Asia WGS

AF:

0.112

AC:

389

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.030

DANN

Benign

0.41

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000014

dbscSNV1_RF

Benign

0.046

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

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