chr15-81279640-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_172217.5(IL16):c.947C>T(p.Pro316Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000044 in 1,614,146 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000045 ( 0 hom. )
Consequence
IL16
NM_172217.5 missense
NM_172217.5 missense
Scores
1
16
Clinical Significance
Conservation
PhyloP100: 3.88
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.12271029).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL16 | NM_172217.5 | c.947C>T | p.Pro316Leu | missense_variant | 8/19 | ENST00000683961.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL16 | ENST00000683961.1 | c.947C>T | p.Pro316Leu | missense_variant | 8/19 | NM_172217.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152278Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249300Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135274
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GnomAD4 exome AF: 0.0000451 AC: 66AN: 1461868Hom.: 0 Cov.: 32 AF XY: 0.0000509 AC XY: 37AN XY: 727236
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GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74398
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2021 | The c.947C>T (p.P316L) alteration is located in exon 7 (coding exon 7) of the IL16 gene. This alteration results from a C to T substitution at nucleotide position 947, causing the proline (P) at amino acid position 316 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
0.028, 0.016
.;B;B
Vest4
0.38, 0.41
MVP
MPC
0.13
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at