chr15-81294587-G-C

Variant names:

• chr15-81294587-G-C
• rs17875491
• NM_172217.5:c.1902+1550G>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.1902+1550G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,118 control chromosomes in the GnomAD database, including 3,100 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 0.19 (3100 hom., cov: 32)
• Consequence: IL16 NM_172217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL16	NM_172217.5	c.1902+1550G>C		intron_variant	Intron 12 of 18	ENST00000683961.1	NP_757366.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000683961.1	c.1902+1550G>C		intron_variant	Intron 12 of 18		NM_172217.5	ENSP00000508085.1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28515 AN: 152000 Hom.: 3103 Cov.: 32

Gnomad AFR AF: 0.0793

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.187 AC: 28520 AN: 152118 Hom.: 3100 Cov.: 32 AF XY: 0.187 AC XY: 13922 AN XY: 74358

African (AFR) AF: 0.0794 AC: 3298 AN: 41536

American (AMR) AF: 0.154 AC: 2355 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 820 AN: 3462

East Asian (EAS) AF: 0.256 AC: 1320 AN: 5154

South Asian (SAS) AF: 0.172 AC: 829 AN: 4820

European-Finnish (FIN) AF: 0.281 AC: 2972 AN: 10576

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16253 AN: 67970

Other (OTH) AF: 0.196 AC: 414 AN: 2112

Alfa AF: 0.131 Hom.: 279

Bravo AF: 0.172

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.55
PhyloP100		0.68
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: rs17875491; hg19: chr15-81586928;