NM_172217.5:c.-102+9478T>C

Variant names:

• chr15-81206630-T-C
• rs1912124
• NM_172217.5:c.-102+9478T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
IL16	NM_172217.5	c.-102+9478T>C		intron_variant	Intron 1 of 18	ENST00000683961.1	NP_757366.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000683961.1	c.-102+9478T>C		intron_variant	Intron 1 of 18		NM_172217.5	ENSP00000508085.1

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

African (AFR) AF: 0.0516 AC: 2139 AN: 41482

American (AMR) AF: 0.0892 AC: 1363 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0834 AC: 289 AN: 3466

East Asian (EAS) AF: 0.0620 AC: 321 AN: 5174

South Asian (SAS) AF: 0.0392 AC: 189 AN: 4816

European-Finnish (FIN) AF: 0.110 AC: 1164 AN: 10564

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0943 AC: 6416 AN: 68004

Other (OTH) AF: 0.0933 AC: 197 AN: 2112

Alfa AF: 0.0922 Hom.: 1299

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
PhyloP100		-0.036
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1912124; hg19: chr15-81498971;