rs7175701

Positions:

• chr15-81266282-T-C

Variant summary

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

The NM_172217.5(IL16):​c.564+481T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,154 control chromosomes in the GnomAD database, including 7,840 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 0.29 (7840 hom., cov: 33)
• Consequence: IL16 NM_172217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL16	NM_172217.5	c.564+481T>C		intron_variant		ENST00000683961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL16	ENST00000683961.1	c.564+481T>C		intron_variant			NM_172217.5	A2

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43364 AN: 152036 Hom.: 7812 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0378

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.286 AC: 43449 AN: 152154 Hom.: 7840 Cov.: 33 AF XY: 0.280 AC XY: 20827 AN XY: 74380

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0378

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.269

Alfa AF: 0.258 Hom.: 949

Bravo AF: 0.293

Asia WGS AF: 0.130 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.56

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: rs7175701; hg19: chr15-81558623;