rs11638444

Positions:

• chr15-81242479-T-C
• chr15-81242479-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.312+16768T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,058 control chromosomes in the GnomAD database, including 4,897 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 0.24 (4897 hom., cov: 32)
• Consequence: IL16 NM_172217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL16	NM_172217.5	c.312+16768T>C		intron_variant		ENST00000683961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL16	ENST00000683961.1	c.312+16768T>C		intron_variant			NM_172217.5	A2

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35867 AN: 151940 Hom.: 4884 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0194

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.236 AC: 35918 AN: 152058 Hom.: 4897 Cov.: 32 AF XY: 0.232 AC XY: 17265 AN XY: 74324

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0194

Gnomad4 SAS AF: 0.0913

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.226

Alfa AF: 0.116 Hom.: 200

Bravo AF: 0.239

Asia WGS AF: 0.104 AC: 362 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.1
DANN	Benign	0.89

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: rs11638444; hg19: chr15-81534820;