rs12907134

Positions:

• chr15-81232978-G-A

Variant summary

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

The NM_172217.5(IL16):​c.312+7267G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,896 control chromosomes in the GnomAD database, including 18,734 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 0.49 (18734 hom., cov: 32)
• Consequence: IL16 NM_172217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL16	NM_172217.5	c.312+7267G>A		intron_variant		ENST00000683961.1	NP_757366.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000683961.1	c.312+7267G>A		intron_variant			NM_172217.5	ENSP00000508085.1

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73854 AN: 151776 Hom.: 18741 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.486 AC: 73862 AN: 151896 Hom.: 18734 Cov.: 32 AF XY: 0.483 AC XY: 35860 AN XY: 74242

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.505

Alfa AF: 0.553 Hom.: 46526

Bravo AF: 0.490

Asia WGS AF: 0.393 AC: 1362 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.75

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: rs12907134; hg19: chr15-81525319;