rs7172689

Variant summary

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

The NM_172217.5(IL16):​c.312+15643C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,684 control chromosomes in the GnomAD database, including 4,928 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 0.24 ( 4928 hom., cov: 32)

Consequence

IL16
NM_172217.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL16NM_172217.5 linkuse as main transcriptc.312+15643C>T intron_variant ENST00000683961.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL16ENST00000683961.1 linkuse as main transcriptc.312+15643C>T intron_variant NM_172217.5 A2Q14005-1

Frequencies

GnomAD3 genomes
AF:
0.237
AC:
35903
AN:
151572
Hom.:
4916
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.374
Gnomad AMI
AF:
0.228
Gnomad AMR
AF:
0.160
Gnomad ASJ
AF:
0.190
Gnomad EAS
AF:
0.0195
Gnomad SAS
AF:
0.0908
Gnomad FIN
AF:
0.227
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.202
Gnomad OTH
AF:
0.221
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.237
AC:
35954
AN:
151684
Hom.:
4928
Cov.:
32
AF XY:
0.233
AC XY:
17276
AN XY:
74112
show subpopulations
Gnomad4 AFR
AF:
0.374
Gnomad4 AMR
AF:
0.160
Gnomad4 ASJ
AF:
0.190
Gnomad4 EAS
AF:
0.0196
Gnomad4 SAS
AF:
0.0915
Gnomad4 FIN
AF:
0.227
Gnomad4 NFE
AF:
0.202
Gnomad4 OTH
AF:
0.227
Alfa
AF:
0.201
Hom.:
2213
Bravo
AF:
0.239
Asia WGS
AF:
0.104
AC:
362
AN:
3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.25
DANN
Benign
0.55

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.

Other links and lift over

dbSNP: rs7172689; hg19: chr15-81533695; API