rs11073001

Variant names:

• chr15-81300461-A-G
• rs11073001
• NM_172217.5:c.3135A>G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_172217.5(IL16):​c.3135A>G​(p.Thr1045Thr) 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
• Publications: 29 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 -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 rank	MANE	Protein	UniProt
IL16	NM_172217.5	c.3135A>G	p.Thr1045Thr	synonymous_variant	Exon 14 of 19	ENST00000683961.1	NP_757366.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000683961.1	c.3135A>G	p.Thr1045Thr	synonymous_variant	Exon 14 of 19		NM_172217.5	ENSP00000508085.1

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

GnomAD2 exomes AF: 0.203 AC: 50562 AN: 248874 AF XY: 0.194

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 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

African (AFR) AF: 0.496 AC: 16584 AN: 33418

American (AMR) AF: 0.215 AC: 9605 AN: 44662

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 5115 AN: 26066

East Asian (EAS) AF: 0.221 AC: 8757 AN: 39632

South Asian (SAS) AF: 0.137 AC: 11793 AN: 86196

European-Finnish (FIN) AF: 0.110 AC: 5873 AN: 53316

Middle Eastern (MID) AF: 0.244 AC: 1404 AN: 5758

European-Non Finnish (NFE) AF: 0.207 AC: 229740 AN: 1109470

Other (OTH) AF: 0.215 AC: 12931 AN: 60258

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

African (AFR) AF: 0.488 AC: 20209 AN: 41442

American (AMR) AF: 0.228 AC: 3483 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3468

East Asian (EAS) AF: 0.212 AC: 1095 AN: 5174

South Asian (SAS) AF: 0.144 AC: 695 AN: 4822

European-Finnish (FIN) AF: 0.0869 AC: 921 AN: 10604

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13043 AN: 67974

Other (OTH) AF: 0.269 AC: 568 AN: 2110

Alfa AF: 0.229 Hom.: 18002

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
PhyloP100		-2.2
Mutation Taster		=99/1	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: rs11073001; hg19: chr15-81592802; COSMIC: COSV57265945; COSMIC: COSV57265945;