rs11073001
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_172217.5(IL16):āc.3135A>Gā(p.Thr1045=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,610,850 control chromosomes in the GnomAD database, including 40,544 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: š 0.27 ( 6926 hom., cov: 32)
Exomes š: 0.21 ( 33618 hom. )
Consequence
IL16
NM_172217.5 synonymous
NM_172217.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.17
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 Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP7
?
Synonymous conserved (PhyloP=-2.16 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL16 | NM_172217.5 | c.3135A>G | p.Thr1045= | synonymous_variant | 14/19 | ENST00000683961.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL16 | ENST00000683961.1 | c.3135A>G | p.Thr1045= | synonymous_variant | 14/19 | NM_172217.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.269 AC: 40861AN: 151956Hom.: 6888 Cov.: 32
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GnomAD3 exomes AF: 0.203 AC: 50562AN: 248874Hom.: 6071 AF XY: 0.194 AC XY: 26131AN XY: 134736
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GnomAD4 exome AF: 0.207 AC: 301802AN: 1458776Hom.: 33618 Cov.: 32 AF XY: 0.203 AC XY: 147113AN XY: 725462
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GnomAD4 genome ? AF: 0.269 AC: 40950AN: 152074Hom.: 6926 Cov.: 32 AF XY: 0.259 AC XY: 19273AN XY: 74350
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at