rs1803275

Variant names:

• chr15-81306075-G-A
• rs1803275
• NM_172217.5:c.3588G>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_172217.5(IL16):​c.3588G>A​(p.Arg1196Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0934 in 1,614,078 control chromosomes in the GnomAD database, including 8,280 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 0.12 (1328 hom., cov: 33)
  • Exomes 𝑓: 0.091 (6952 hom.)
• Consequence: IL16 NM_172217.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99
• Publications: 20 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BP7: Synonymous conserved (PhyloP=1.99 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 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.3588G>A	p.Arg1196Arg	synonymous	Exon 17 of 19	NP_757366.2	Q14005-1
	IL16	NM_001352686.2		c.3741G>A	p.Arg1247Arg	synonymous	Exon 17 of 19	NP_001339615.1
	IL16	NM_001438661.1		c.3729G>A	p.Arg1243Arg	synonymous	Exon 17 of 19	NP_001425590.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL16	ENST00000683961.1	MANE Select	c.3588G>A	p.Arg1196Arg	synonymous	Exon 17 of 19	ENSP00000508085.1	Q14005-1
	IL16	ENST00000302987.10	TSL:1	c.3729G>A	p.Arg1243Arg	synonymous	Exon 17 of 19	ENSP00000302935.5	A0A8C8KBU6
	IL16	ENST00000394652.6	TSL:1	c.1485G>A	p.Arg495Arg	synonymous	Exon 5 of 7	ENSP00000378147.2	Q14005-3

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17750 AN: 152128 Hom.: 1325 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0597

Gnomad FIN AF: 0.0303

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0781

Gnomad OTH AF: 0.111

GnomAD2 exomes AF: 0.0964 AC: 24222 AN: 251352 AF XY: 0.0894

Gnomad AFR exome AF: 0.206

Gnomad AMR exome AF: 0.140

Gnomad ASJ exome AF: 0.0538

Gnomad EAS exome AF: 0.182

Gnomad FIN exome AF: 0.0371

Gnomad NFE exome AF: 0.0812

Gnomad OTH exome AF: 0.0868

GnomAD4 exome AF: 0.0910 AC: 133019 AN: 1461832 Hom.: 6952 Cov.: 32 AF XY: 0.0888 AC XY: 64572 AN XY: 727232

African (AFR) AF: 0.213 AC: 7126 AN: 33478

American (AMR) AF: 0.141 AC: 6288 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.0537 AC: 1404 AN: 26136

East Asian (EAS) AF: 0.181 AC: 7182 AN: 39700

South Asian (SAS) AF: 0.0536 AC: 4626 AN: 86258

European-Finnish (FIN) AF: 0.0427 AC: 2278 AN: 53388

Middle Eastern (MID) AF: 0.0600 AC: 346 AN: 5768

European-Non Finnish (NFE) AF: 0.0881 AC: 98018 AN: 1111984

Other (OTH) AF: 0.0952 AC: 5751 AN: 60396

GnomAD4 genome AF: 0.117 AC: 17770 AN: 152246 Hom.: 1328 Cov.: 33 AF XY: 0.112 AC XY: 8361 AN XY: 74434

African (AFR) AF: 0.205 AC: 8522 AN: 41524

American (AMR) AF: 0.125 AC: 1907 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3470

East Asian (EAS) AF: 0.176 AC: 911 AN: 5178

South Asian (SAS) AF: 0.0597 AC: 288 AN: 4822

European-Finnish (FIN) AF: 0.0303 AC: 322 AN: 10612

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0781 AC: 5309 AN: 68018

Other (OTH) AF: 0.110 AC: 232 AN: 2116

Alfa AF: 0.0926 Hom.: 1225

Bravo AF: 0.131

Asia WGS AF: 0.118 AC: 411 AN: 3478

EpiCase AF: 0.0782

EpiControl AF: 0.0794

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	8.9
DANN	Benign	0.51
PhyloP100		2.0
Mutation Taster		=99/1	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: rs1803275; hg19: chr15-81598416; COSMIC: COSV57155272; COSMIC: COSV57155272;