chr15-81294587-G-C

Position:

• chr15-81294587-G-C

Variant summary

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

The NM_172217.5(IL16):​c.1902+1550G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,118 control chromosomes in the GnomAD database, including 3,100 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 0.19 (3100 hom., cov: 32)
• Consequence: IL16 NM_172217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL16	NM_172217.5	c.1902+1550G>C		intron_variant		ENST00000683961.1	NP_757366.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000683961.1	c.1902+1550G>C		intron_variant			NM_172217.5	ENSP00000508085	A2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28515 AN: 152000 Hom.: 3103 Cov.: 32

Gnomad AFR AF: 0.0793

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.187 AC: 28520 AN: 152118 Hom.: 3100 Cov.: 32 AF XY: 0.187 AC XY: 13922 AN XY: 74358

Gnomad4 AFR AF: 0.0794

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.196

Alfa AF: 0.131 Hom.: 279

Bravo AF: 0.172

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.55

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: rs17875491; hg19: chr15-81586928;