NM_172217.5:c.1420+258G>T

Variant names:

• chr15-81290798-G-T
• rs7170924
• NM_172217.5:c.1420+258G>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.1420+258G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,034 control chromosomes in the GnomAD database, including 7,530 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 (7530 hom., cov: 32)
• Consequence: IL16 NM_172217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 16 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL16	NM_172217.5	c.1420+258G>T		intron_variant	Intron 11 of 18	ENST00000683961.1	NP_757366.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000683961.1	c.1420+258G>T		intron_variant	Intron 11 of 18		NM_172217.5	ENSP00000508085.1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45875 AN: 151914 Hom.: 7515 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.302 AC: 45941 AN: 152034 Hom.: 7530 Cov.: 32 AF XY: 0.309 AC XY: 22939 AN XY: 74332

African (AFR) AF: 0.375 AC: 15563 AN: 41474

American (AMR) AF: 0.297 AC: 4538 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3470

East Asian (EAS) AF: 0.502 AC: 2598 AN: 5174

South Asian (SAS) AF: 0.464 AC: 2224 AN: 4796

European-Finnish (FIN) AF: 0.299 AC: 3162 AN: 10564

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16102 AN: 67950

Other (OTH) AF: 0.283 AC: 598 AN: 2112

Alfa AF: 0.260 Hom.: 9820

Bravo AF: 0.301

Asia WGS AF: 0.510 AC: 1772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.047
DANN	Benign	0.71
PhyloP100		-0.83
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: rs7170924; hg19: chr15-81583139;