rs7182786

Positions:

• chr15-81181923-A-G
• chr15-81181923-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560989.1(IL16):​n.427-842A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,010 control chromosomes in the GnomAD database, including 9,523 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 0.30 (9523 hom., cov: 32)
• Consequence: IL16 ENST00000560989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.743

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000560989.1	n.427-842A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44815 AN: 151892 Hom.: 9482 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.295 AC: 44907 AN: 152010 Hom.: 9523 Cov.: 32 AF XY: 0.298 AC XY: 22174 AN XY: 74298

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.266

Alfa AF: 0.0712 Hom.: 101

Bravo AF: 0.326

Asia WGS AF: 0.532 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.9
DANN	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7182786; hg19: chr15-81474264;