rs11073001

chr15-81300461-A-G

Variant summary

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

The NM_172217.5(IL16):c.3135A>G(p.Thr1045=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,610,850 control chromosomes in the GnomAD database, including 40,544 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 0.27 (6926 hom., cov: 32)
  • Exomes 𝑓: 0.21 (33618 hom.)
• Consequence: IL16 NM_172217.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

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=-0.93).
• BP7: Synonymous conserved (PhyloP=-2.16 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL16	NM_172217.5	c.3135A>G	p.Thr1045=	synonymous_variant	14/19	ENST00000683961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL16	ENST00000683961.1	c.3135A>G	p.Thr1045=	synonymous_variant	14/19		NM_172217.5	A2

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40861 AN: 151956 Hom.: 6888 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.263

GnomAD3 exomes AF: 0.203 AC: 50562 AN: 248874 Hom.: 6071 AF XY: 0.194 AC XY: 26131 AN XY: 134736

Gnomad AFR exome AF: 0.489

Gnomad AMR exome AF: 0.208

Gnomad ASJ exome AF: 0.194

Gnomad EAS exome AF: 0.221

Gnomad SAS exome AF: 0.134

Gnomad FIN exome AF: 0.0970

Gnomad NFE exome AF: 0.198

Gnomad OTH exome AF: 0.198

GnomAD4 exome AF: 0.207 AC: 301802 AN: 1458776 Hom.: 33618 Cov.: 32 AF XY: 0.203 AC XY: 147113 AN XY: 725462

Gnomad4 AFR exome AF: 0.496

Gnomad4 AMR exome AF: 0.215

Gnomad4 ASJ exome AF: 0.196

Gnomad4 EAS exome AF: 0.221

Gnomad4 SAS exome AF: 0.137

Gnomad4 FIN exome AF: 0.110

Gnomad4 NFE exome AF: 0.207

Gnomad4 OTH exome AF: 0.215

GnomAD4 genome AF: 0.269 AC: 40950 AN: 152074 Hom.: 6926 Cov.: 32 AF XY: 0.259 AC XY: 19273 AN XY: 74350

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0869

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.269

Alfa AF: 0.220 Hom.: 6436

Bravo AF: 0.294

Asia WGS AF: 0.213 AC: 740 AN: 3478

EpiCase AF: 0.202

EpiControl AF: 0.204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.018
Dann	Benign	0.37

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: rs11073001; hg19: chr15-81592802; COSMIC: COSV57265945; COSMIC: COSV57265945;