15-81293722-C-T

Variant names:

• chr15-81293722-C-T
• rs17875486
• NM_172217.5:c.1902+685C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_172217.5(IL16):​c.1902+685C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,088 control chromosomes in the GnomAD database, including 14,039 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 0.42 (14039 hom., cov: 32)
• Consequence: IL16 NM_172217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_172217.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL16	NM_172217.5	MANE Select	c.1902+685C>T		intron	N/A	NP_757366.2
	IL16	NM_001352686.2		c.2055+685C>T		intron	N/A	NP_001339615.1
	IL16	NM_001438661.1		c.2043+685C>T		intron	N/A	NP_001425590.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL16	ENST00000683961.1	MANE Select	c.1902+685C>T		intron	N/A	ENSP00000508085.1
	IL16	ENST00000302987.10	TSL:1	c.2043+685C>T		intron	N/A	ENSP00000302935.5
	IL16	ENST00000394660.6	TSL:2	c.1902+685C>T		intron	N/A	ENSP00000378155.2

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63945 AN: 151970 Hom.: 14048 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.420 AC: 63945 AN: 152088 Hom.: 14039 Cov.: 32 AF XY: 0.418 AC XY: 31051 AN XY: 74350

African (AFR) AF: 0.315 AC: 13049 AN: 41474

American (AMR) AF: 0.453 AC: 6935 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1696 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1415 AN: 5166

South Asian (SAS) AF: 0.311 AC: 1499 AN: 4822

European-Finnish (FIN) AF: 0.445 AC: 4697 AN: 10566

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33132 AN: 67972

Other (OTH) AF: 0.422 AC: 891 AN: 2110

Alfa AF: 0.455 Hom.: 25999

Bravo AF: 0.419

Asia WGS AF: 0.249 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.45
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17875486; hg19: chr15-81586063;