rs1912124

chr15-81206630-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.-102+9478T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0806 in 152,102 control chromosomes in the GnomAD database, including 516 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 0.081 (516 hom., cov: 32)
• Consequence: IL16 NM_172217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

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=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL16	NM_172217.5	c.-102+9478T>C		intron_variant		ENST00000683961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL16	ENST00000683961.1	c.-102+9478T>C		intron_variant			NM_172217.5	A2

Frequencies

GnomAD3 genomes AF: 0.0806 AC: 12243 AN: 151984 Hom.: 516 Cov.: 32

Gnomad AFR AF: 0.0518

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0891

Gnomad ASJ AF: 0.0834

Gnomad EAS AF: 0.0619

Gnomad SAS AF: 0.0390

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.0885

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

GnomAD4 genome AF: 0.0806 AC: 12253 AN: 152102 Hom.: 516 Cov.: 32 AF XY: 0.0806 AC XY: 5990 AN XY: 74358

Gnomad4 AFR AF: 0.0516

Gnomad4 AMR AF: 0.0892

Gnomad4 ASJ AF: 0.0834

Gnomad4 EAS AF: 0.0620

Gnomad4 SAS AF: 0.0392

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.0943

Gnomad4 OTH AF: 0.0933

Alfa AF: 0.0934 Hom.: 948

Bravo AF: 0.0810

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
Cadd	Benign	9.6
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1912124; hg19: chr15-81498971;