15-81191389-G-C

Position:

• chr15-81191389-G-C

Variant summary

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

The ENST00000302987.10(IL16):​c.40+8493G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,106 control chromosomes in the GnomAD database, including 16,285 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 0.41 (16285 hom., cov: 33)
• Consequence: IL16 ENST00000302987.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL16	XM_047432447.1	c.91+2986G>C		intron_variant			XP_047288403.1
IL16	XM_047432448.1	c.91+2986G>C		intron_variant			XP_047288404.1
IL16	XM_047432449.1	c.40+8493G>C		intron_variant			XP_047288405.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000302987.10	c.40+8493G>C		intron_variant		1		ENSP00000302935.5
IL16	ENST00000360547.9	n.-102+2986G>C		intron_variant		2		ENSP00000456972.1
IL16	ENST00000560241.5	n.-102+8493G>C		intron_variant		2		ENSP00000452738.1

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61950 AN: 151986 Hom.: 16230 Cov.: 33

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.408 AC: 62073 AN: 152106 Hom.: 16285 Cov.: 33 AF XY: 0.412 AC XY: 30619 AN XY: 74368

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.377

Alfa AF: 0.308 Hom.: 1179

Bravo AF: 0.438

Asia WGS AF: 0.626 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8028364; hg19: chr15-81483730;