rs11857713

Positions:

• chr15-81298924-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_172217.5(IL16):​c.2054-456C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,256 control chromosomes in the GnomAD database, including 1,458 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 (1458 hom., cov: 33)
• Consequence: IL16 NM_172217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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]

ACMG classification

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 = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL16	NM_172217.5	c.2054-456C>T		intron_variant		ENST00000683961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL16	ENST00000683961.1	c.2054-456C>T		intron_variant			NM_172217.5	A2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17770 AN: 152138 Hom.: 1451 Cov.: 33

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0587

Gnomad FIN AF: 0.0288

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.108

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.117 AC: 17796 AN: 152256 Hom.: 1458 Cov.: 33 AF XY: 0.113 AC XY: 8412 AN XY: 74440

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.0586

Gnomad4 FIN AF: 0.0288

Gnomad4 NFE AF: 0.0665

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0770 Hom.: 1176

Bravo AF: 0.131

Asia WGS AF: 0.111 AC: 385 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	0.44
DANN	Benign	0.55

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

LitVar

Other links and lift over

dbSNP: rs11857713; hg19: chr15-81591265;