15-81304249-T-G

Variant names:

• chr15-81304249-T-G
• rs3848180
• NM_172217.5:c.3420+599T>G

Variant summary

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

The NM_001352686.2(IL16):​c.3573+599T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,064 control chromosomes in the GnomAD database, including 19,740 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 0.50 (19740 hom., cov: 33)
• Consequence: IL16 NM_001352686.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 24 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]

ENSG00000271725 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352686.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL16	NM_172217.5	MANE Select	c.3420+599T>G		intron	N/A	NP_757366.2
	IL16	NM_001352686.2		c.3573+599T>G		intron	N/A	NP_001339615.1
	IL16	NM_001438661.1		c.3561+599T>G		intron	N/A	NP_001425590.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL16	ENST00000683961.1	MANE Select	c.3420+599T>G		intron	N/A	ENSP00000508085.1
	IL16	ENST00000302987.10	TSL:1	c.3561+599T>G		intron	N/A	ENSP00000302935.5
	IL16	ENST00000394652.6	TSL:1	c.1317+599T>G		intron	N/A	ENSP00000378147.2

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75255 AN: 151946 Hom.: 19695 Cov.: 33

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.495 AC: 75347 AN: 152064 Hom.: 19740 Cov.: 33 AF XY: 0.484 AC XY: 35951 AN XY: 74318

African (AFR) AF: 0.681 AC: 28260 AN: 41486

American (AMR) AF: 0.401 AC: 6120 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3468

East Asian (EAS) AF: 0.495 AC: 2560 AN: 5168

South Asian (SAS) AF: 0.298 AC: 1436 AN: 4820

European-Finnish (FIN) AF: 0.368 AC: 3891 AN: 10570

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.439 AC: 29849 AN: 67960

Other (OTH) AF: 0.496 AC: 1049 AN: 2114

Alfa AF: 0.452 Hom.: 27634

Bravo AF: 0.510

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.40
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: rs3848180; hg19: chr15-81596590;