15-81304249-T-G

Position:

• chr15-81304249-T-G

Variant summary

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

The NM_172217.5(IL16):​c.3420+599T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,064 control chromosomes in the GnomAD database, including 19,740 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 0.50 (19740 hom., cov: 33)
• Consequence: IL16 NM_172217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL16	NM_172217.5	c.3420+599T>G		intron_variant		ENST00000683961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL16	ENST00000683961.1	c.3420+599T>G		intron_variant			NM_172217.5	A2
	ENST00000607019.1	n.62-620A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75255 AN: 151946 Hom.: 19695 Cov.: 33

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.495 AC: 75347 AN: 152064 Hom.: 19740 Cov.: 33 AF XY: 0.484 AC XY: 35951 AN XY: 74318

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.496

Alfa AF: 0.439 Hom.: 18138

Bravo AF: 0.510

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: rs3848180; hg19: chr15-81596590;