15-81308999-G-T

Position:

• chr15-81308999-G-T

Variant summary

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

The NM_172217.5(IL16):​c.*201G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 488,574 control chromosomes in the GnomAD database, including 9,820 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 0.22 (5102 hom., cov: 34)
  • Exomes 𝑓: 0.16 (4718 hom.)
• Consequence: IL16 NM_172217.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL16	NM_172217.5	c.*201G>T		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.*201G>T		3_prime_UTR_variant	19/19		NM_172217.5	ENSP00000508085	A2
	ENST00000607019.1	n.61+332C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34151 AN: 152128 Hom.: 5078 Cov.: 34

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.224

GnomAD4 exome AF: 0.158 AC: 53151 AN: 336328 Hom.: 4718 Cov.: 3 AF XY: 0.155 AC XY: 27154 AN XY: 174658

Gnomad4 AFR exome AF: 0.422

Gnomad4 AMR exome AF: 0.211

Gnomad4 ASJ exome AF: 0.186

Gnomad4 EAS exome AF: 0.212

Gnomad4 SAS exome AF: 0.133

Gnomad4 FIN exome AF: 0.0858

Gnomad4 NFE exome AF: 0.146

Gnomad4 OTH exome AF: 0.183

GnomAD4 genome AF: 0.225 AC: 34225 AN: 152246 Hom.: 5102 Cov.: 34 AF XY: 0.218 AC XY: 16206 AN XY: 74446

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0673

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.230

Alfa AF: 0.168 Hom.: 2402

Bravo AF: 0.248

Asia WGS AF: 0.200 AC: 693 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	0.27
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11325; hg19: chr15-81601340;