rs12438640

Variant summary

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

The NM_172217.5(IL16):​c.-101-1378G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,158 control chromosomes in the GnomAD database, including 1,981 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 0.14 ( 1981 hom., cov: 32)

Consequence

IL16
NM_172217.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.33
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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IL16NM_172217.5 linkc.-101-1378G>A intron_variant ENST00000683961.1 NP_757366.2 Q14005-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IL16ENST00000683961.1 linkc.-101-1378G>A intron_variant NM_172217.5 ENSP00000508085.1 Q14005-1

Frequencies

GnomAD3 genomes
AF:
0.142
AC:
21567
AN:
152040
Hom.:
1970
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.142
Gnomad AMI
AF:
0.0208
Gnomad AMR
AF:
0.251
Gnomad ASJ
AF:
0.0938
Gnomad EAS
AF:
0.369
Gnomad SAS
AF:
0.316
Gnomad FIN
AF:
0.113
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.0970
Gnomad OTH
AF:
0.130
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.142
AC:
21611
AN:
152158
Hom.:
1981
Cov.:
32
AF XY:
0.149
AC XY:
11094
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.142
Gnomad4 AMR
AF:
0.252
Gnomad4 ASJ
AF:
0.0938
Gnomad4 EAS
AF:
0.370
Gnomad4 SAS
AF:
0.316
Gnomad4 FIN
AF:
0.113
Gnomad4 NFE
AF:
0.0970
Gnomad4 OTH
AF:
0.129
Alfa
AF:
0.127
Hom.:
843
Bravo
AF:
0.152
Asia WGS
AF:
0.326
AC:
1132
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.058
DANN
Benign
0.39

Splicing

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: rs12438640; hg19: chr15-81516262; API