rs4128767

Variant names:

• chr15-81251066-A-G
• rs4128767
• NM_172217.5:c.313-8706A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-81251066-A-G
• chr15-81251066-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_172217.5(IL16):​c.313-8706A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,946 control chromosomes in the GnomAD database, including 15,307 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 0.42 (15307 hom., cov: 32)
• Consequence: IL16 NM_172217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 10 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL16	NM_172217.5	c.313-8706A>G		intron_variant	Intron 2 of 18	ENST00000683961.1	NP_757366.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000683961.1	c.313-8706A>G		intron_variant	Intron 2 of 18		NM_172217.5	ENSP00000508085.1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63821 AN: 151828 Hom.: 15258 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.421 AC: 63943 AN: 151946 Hom.: 15307 Cov.: 32 AF XY: 0.422 AC XY: 31377 AN XY: 74274

African (AFR) AF: 0.670 AC: 27737 AN: 41408

American (AMR) AF: 0.363 AC: 5535 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1174 AN: 3470

East Asian (EAS) AF: 0.218 AC: 1127 AN: 5172

South Asian (SAS) AF: 0.393 AC: 1897 AN: 4826

European-Finnish (FIN) AF: 0.382 AC: 4030 AN: 10554

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21295 AN: 67952

Other (OTH) AF: 0.386 AC: 814 AN: 2108

Alfa AF: 0.344 Hom.: 8143

Bravo AF: 0.429

Asia WGS AF: 0.382 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.76
PhyloP100		-1.8
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: rs4128767; hg19: chr15-81543407;