Variant chr15-81306075-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_172217.5(IL16):c.3588G>A(p.Arg1196=) 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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.99

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:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL16	NM_172217.5 linkuse as main transcript	c.3588G>A	p.Arg1196=	synonymous_variant	17/19	ENST00000683961.1	NP_757366.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL16	ENST00000683961.1 linkuse as main transcript	c.3588G>A	p.Arg1196=	synonymous_variant	17/19		NM_172217.5	ENSP00000508085	A2	Q14005-1
	ENST00000607019.1 linkuse as main transcript	n.62-2446C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17750

AN:

152128

Hom.:

1325

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.0964

AC:

24222

AN:

251352

Hom.:

1499

AF XY:

0.0894

AC XY:

12139

AN XY:

135852

show subpopulations

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 SAS exome

AF:

0.0517

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.:

AF XY:

0.0888

AC XY:

64572

AN XY:

727232

show subpopulations

Gnomad4 AFR exome

AF:

0.213

Gnomad4 AMR exome

AF:

0.141

Gnomad4 ASJ exome

AF:

0.0537

Gnomad4 EAS exome

AF:

0.181

Gnomad4 SAS exome

AF:

0.0536

Gnomad4 FIN exome

AF:

0.0427

Gnomad4 NFE exome

AF:

0.0881

Gnomad4 OTH exome

AF:

0.0952

GnomAD4 genome

AF:

0.117

AC:

17770

AN:

152246

Hom.:

1328

Cov.:

AF XY:

0.112

AC XY:

8361

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.205

Gnomad4 AMR

AF:

0.125

Gnomad4 ASJ

AF:

0.0536

Gnomad4 EAS

AF:

0.176

Gnomad4 SAS

AF:

0.0597

Gnomad4 FIN

AF:

0.0303

Gnomad4 NFE

AF:

0.0781

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.0876

Hom.:

867

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

8.9

DANN

Benign

0.51

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