dbSNP rs8031107: IL16:p.Gln469Gln (chr15-81290527-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.07

Variant links:

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]

IL16 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL16	NM_172217.5 link	c.1407G>A	p.Gln469Gln	synonymous_variant	Exon 11 of 19	ENST00000683961.1	NP_757366.2	Q14005-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000683961.1 link	c.1407G>A	p.Gln469Gln	synonymous_variant	Exon 11 of 19		NM_172217.5	ENSP00000508085.1		Q14005-1

Frequencies

GnomAD3 genomes

AF:

0.529

AC:

80272

AN:

151830

Hom.:

22077

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.504

AC:

125049

AN:

248208

Hom.:

32416

AF XY:

0.503

AC XY:

67758

AN XY:

134656

show subpopulations

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 SAS exome

AF:

0.588

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.:

AF XY:

0.467

AC XY:

338477

AN XY:

724176

show subpopulations

Gnomad4 AFR exome

AF:

0.699

Gnomad4 AMR exome

AF:

0.490

Gnomad4 ASJ exome

AF:

0.498

Gnomad4 EAS exome

AF:

0.497

Gnomad4 SAS exome

AF:

0.582

Gnomad4 FIN exome

AF:

0.523

Gnomad4 NFE exome

AF:

0.440

Gnomad4 OTH exome

AF:

0.487

GnomAD4 genome

AF:

0.529

AC:

80393

AN:

151948

Hom.:

22133

Cov.:

AF XY:

0.531

AC XY:

39468

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.686

Gnomad4 AMR

AF:

0.459

Gnomad4 ASJ

AF:

0.515

Gnomad4 EAS

AF:

0.537

Gnomad4 SAS

AF:

0.597

Gnomad4 FIN

AF:

0.530

Gnomad4 NFE

AF:

0.447

Gnomad4 OTH

AF:

0.521

Alfa

AF:

0.468

Hom.:

34329

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

4.9

DANN

Benign

0.59

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over