rs859

Positions:

• chr15-81308981-A-G

Variant summary

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

The NM_172217.5(IL16):​c.*183A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 517,678 control chromosomes in the GnomAD database, including 24,585 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 0.33 (9104 hom., cov: 33)
  • Exomes 𝑓: 0.28 (15481 hom.)
• Consequence: IL16 NM_172217.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL16	NM_172217.5	c.*183A>G		3_prime_UTR_variant	19/19	ENST00000683961.1	NP_757366.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000683961.1	c.*183A>G		3_prime_UTR_variant	19/19		NM_172217.5	ENSP00000508085	A2
	ENST00000607019.1	n.61+350T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50693 AN: 152108 Hom.: 9089 Cov.: 33

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.334

GnomAD4 exome AF: 0.282 AC: 103234 AN: 365452 Hom.: 15481 Cov.: 4 AF XY: 0.277 AC XY: 52806 AN XY: 190860

Gnomad4 AFR exome AF: 0.475

Gnomad4 AMR exome AF: 0.289

Gnomad4 ASJ exome AF: 0.305

Gnomad4 EAS exome AF: 0.429

Gnomad4 SAS exome AF: 0.193

Gnomad4 FIN exome AF: 0.285

Gnomad4 NFE exome AF: 0.266

Gnomad4 OTH exome AF: 0.307

GnomAD4 genome AF: 0.333 AC: 50746 AN: 152226 Hom.: 9104 Cov.: 33 AF XY: 0.330 AC XY: 24567 AN XY: 74456

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.331

Alfa AF: 0.278 Hom.: 3643

Bravo AF: 0.343

Asia WGS AF: 0.335 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.94
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs859; hg19: chr15-81601322;