rs8031107

Variant names:

• chr15-81290527-G-A
• rs8031107
• NM_172217.5:c.1407G>A

Variant summary

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

The NM_001352684.2(IL16):​c.-613G>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,607,100 control chromosomes in the GnomAD database, including 182,157 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 0.53 (22133 hom., cov: 32)
  • Exomes 𝑓: 0.46 (160024 hom.)
• Consequence: IL16 NM_001352684.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 31 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=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352684.2. 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.1407G>A	p.Gln469Gln	synonymous	Exon 11 of 19	NP_757366.2
	IL16	NM_001352684.2		c.-613G>A		5_prime_UTR_premature_start_codon_gain	Exon 11 of 20	NP_001339613.1
	IL16	NM_001352686.2		c.1560G>A	p.Gln520Gln	synonymous	Exon 11 of 19	NP_001339615.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL16	ENST00000683961.1	MANE Select	c.1407G>A	p.Gln469Gln	synonymous	Exon 11 of 19	ENSP00000508085.1
	IL16	ENST00000302987.10	TSL:1	c.1548G>A	p.Gln516Gln	synonymous	Exon 11 of 19	ENSP00000302935.5
	IL16	ENST00000909975.1		c.1407G>A	p.Gln469Gln	synonymous	Exon 11 of 19	ENSP00000580034.1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80272 AN: 151830 Hom.: 22077 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.516

GnomAD2 exomes AF: 0.504 AC: 125049 AN: 248208 AF XY: 0.503

Gnomad AFR exome AF: 0.690

Gnomad AMR exome AF: 0.492

Gnomad ASJ exome AF: 0.494

Gnomad EAS exome AF: 0.544

Gnomad FIN exome AF: 0.523

Gnomad NFE exome AF: 0.451

Gnomad OTH exome AF: 0.496

GnomAD4 exome AF: 0.464 AC: 675187 AN: 1455152 Hom.: 160024 Cov.: 30 AF XY: 0.467 AC XY: 338477 AN XY: 724176

African (AFR) AF: 0.699 AC: 23306 AN: 33324

American (AMR) AF: 0.490 AC: 21808 AN: 44548

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 12966 AN: 26060

East Asian (EAS) AF: 0.497 AC: 19695 AN: 39616

South Asian (SAS) AF: 0.582 AC: 49979 AN: 85802

European-Finnish (FIN) AF: 0.523 AC: 27902 AN: 53388

Middle Eastern (MID) AF: 0.531 AC: 3053 AN: 5750

European-Non Finnish (NFE) AF: 0.440 AC: 487175 AN: 1106514

Other (OTH) AF: 0.487 AC: 29303 AN: 60150

GnomAD4 genome AF: 0.529 AC: 80393 AN: 151948 Hom.: 22133 Cov.: 32 AF XY: 0.531 AC XY: 39468 AN XY: 74258

African (AFR) AF: 0.686 AC: 28435 AN: 41432

American (AMR) AF: 0.459 AC: 7007 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1786 AN: 3468

East Asian (EAS) AF: 0.537 AC: 2779 AN: 5172

South Asian (SAS) AF: 0.597 AC: 2874 AN: 4816

European-Finnish (FIN) AF: 0.530 AC: 5584 AN: 10530

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.447 AC: 30348 AN: 67954

Other (OTH) AF: 0.521 AC: 1101 AN: 2112

Alfa AF: 0.481 Hom.: 56703

Bravo AF: 0.528

Asia WGS AF: 0.628 AC: 2186 AN: 3478

EpiCase AF: 0.450

EpiControl AF: 0.452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	4.9
DANN	Benign	0.59
PhyloP100		1.1
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: rs8031107; hg19: chr15-81582868; COSMIC: COSV57261232;