15-81242479-T-C

Variant names:

• chr15-81242479-T-C
• rs11638444
• NM_172217.5:c.312+16768T>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.312+16768T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,058 control chromosomes in the GnomAD database, including 4,897 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 0.24 (4897 hom., cov: 32)
• Consequence: IL16 NM_172217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 4 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 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.312+16768T>C		intron	N/A	NP_757366.2
	IL16	NM_001352686.2		c.465+16768T>C		intron	N/A	NP_001339615.1
	IL16	NM_001438661.1		c.453+16768T>C		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.312+16768T>C		intron	N/A	ENSP00000508085.1
	IL16	ENST00000302987.10	TSL:1	c.453+16768T>C		intron	N/A	ENSP00000302935.5
	IL16	ENST00000394660.6	TSL:2	c.312+16768T>C		intron	N/A	ENSP00000378155.2

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35867 AN: 151940 Hom.: 4884 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0194

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.236 AC: 35918 AN: 152058 Hom.: 4897 Cov.: 32 AF XY: 0.232 AC XY: 17265 AN XY: 74324

African (AFR) AF: 0.371 AC: 15395 AN: 41460

American (AMR) AF: 0.159 AC: 2439 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3466

East Asian (EAS) AF: 0.0194 AC: 101 AN: 5194

South Asian (SAS) AF: 0.0913 AC: 441 AN: 4828

European-Finnish (FIN) AF: 0.225 AC: 2381 AN: 10572

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13748 AN: 67924

Other (OTH) AF: 0.226 AC: 478 AN: 2114

Alfa AF: 0.116 Hom.: 200

Bravo AF: 0.239

Asia WGS AF: 0.104 AC: 362 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.1
DANN	Benign	0.89
PhyloP100		0.21
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: rs11638444; hg19: chr15-81534820;