rs8031107

Positions:

• chr15-81290527-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_172217.5(IL16):​c.1407G>A​(p.Gln469=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,607,100 control chromosomes in the GnomAD database, including 182,157 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 0.53 (22133 hom., cov: 32)
  • Exomes 𝑓: 0.46 (160024 hom.)
• Consequence: IL16 NM_172217.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP7: Synonymous conserved (PhyloP=1.07 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL16	NM_172217.5	c.1407G>A	p.Gln469=	synonymous_variant	11/19	ENST00000683961.1	NP_757366.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000683961.1	c.1407G>A	p.Gln469=	synonymous_variant	11/19		NM_172217.5	ENSP00000508085	A2

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80272 AN: 151830 Hom.: 22077 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.516

GnomAD3 exomes AF: 0.504 AC: 125049 AN: 248208 Hom.: 32416 AF XY: 0.503 AC XY: 67758 AN XY: 134656

Gnomad AFR exome AF: 0.690

Gnomad AMR exome AF: 0.492

Gnomad ASJ exome AF: 0.494

Gnomad EAS exome AF: 0.544

Gnomad SAS exome AF: 0.588

Gnomad FIN exome AF: 0.523

Gnomad NFE exome AF: 0.451

Gnomad OTH exome AF: 0.496

GnomAD4 exome AF: 0.464 AC: 675187 AN: 1455152 Hom.: 160024 Cov.: 30 AF XY: 0.467 AC XY: 338477 AN XY: 724176

Gnomad4 AFR exome AF: 0.699

Gnomad4 AMR exome AF: 0.490

Gnomad4 ASJ exome AF: 0.498

Gnomad4 EAS exome AF: 0.497

Gnomad4 SAS exome AF: 0.582

Gnomad4 FIN exome AF: 0.523

Gnomad4 NFE exome AF: 0.440

Gnomad4 OTH exome AF: 0.487

GnomAD4 genome AF: 0.529 AC: 80393 AN: 151948 Hom.: 22133 Cov.: 32 AF XY: 0.531 AC XY: 39468 AN XY: 74258

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.521

Alfa AF: 0.468 Hom.: 34329

Bravo AF: 0.528

Asia WGS AF: 0.628 AC: 2186 AN: 3478

EpiCase AF: 0.450

EpiControl AF: 0.452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	4.9
DANN	Benign	0.59

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

Publications

LitVar

Other links and lift over

dbSNP: rs8031107; hg19: chr15-81582868; COSMIC: COSV57261232;