rs7172689

Variant names:

• chr15-81241354-C-T
• rs7172689
• NM_172217.5:c.312+15643C>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.312+15643C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,684 control chromosomes in the GnomAD database, including 4,928 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 0.24 (4928 hom., cov: 32)
• Consequence: IL16 NM_172217.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 14 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_172217.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL16	NM_172217.5	MANE Select	c.312+15643C>T		intron	N/A	NP_757366.2
	IL16	NM_001352686.2		c.465+15643C>T		intron	N/A	NP_001339615.1
	IL16	NM_001438661.1		c.453+15643C>T		intron	N/A	NP_001425590.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL16	ENST00000683961.1	MANE Select	c.312+15643C>T		intron	N/A	ENSP00000508085.1
	IL16	ENST00000302987.10	TSL:1	c.453+15643C>T		intron	N/A	ENSP00000302935.5
	IL16	ENST00000909975.1		c.312+15643C>T		intron	N/A	ENSP00000580034.1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35903 AN: 151572 Hom.: 4916 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.0908

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.237 AC: 35954 AN: 151684 Hom.: 4928 Cov.: 32 AF XY: 0.233 AC XY: 17276 AN XY: 74112

African (AFR) AF: 0.374 AC: 15496 AN: 41424

American (AMR) AF: 0.160 AC: 2432 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3466

East Asian (EAS) AF: 0.0196 AC: 101 AN: 5164

South Asian (SAS) AF: 0.0915 AC: 440 AN: 4808

European-Finnish (FIN) AF: 0.227 AC: 2378 AN: 10474

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13696 AN: 67808

Other (OTH) AF: 0.227 AC: 478 AN: 2110

Alfa AF: 0.217 Hom.: 5057

Bravo AF: 0.239

Asia WGS AF: 0.104 AC: 362 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.25
DANN	Benign	0.55
PhyloP100		-1.3
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: rs7172689; hg19: chr15-81533695;