rs1051009
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001386809.1(CXCL16):c.*15C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 1,594,374 control chromosomes in the GnomAD database, including 95,233 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 0.28 ( 7356 hom., cov: 32)
Exomes 𝑓: 0.34 ( 87877 hom. )
Consequence
CXCL16
NM_001386809.1 3_prime_UTR
NM_001386809.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.238
Genes affected
CXCL16 (HGNC:16642): (C-X-C motif chemokine ligand 16) Enables chemokine activity. Involved in several processes, including positive regulation of cell growth; response to interferon-gamma; and response to tumor necrosis factor. Located in extracellular space. Biomarker of COVID-19 and systemic scleroderma. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCL16 | NM_001386809.1 | c.*15C>T | 3_prime_UTR_variant | 5/6 | ENST00000293778.12 | ||
CXCL16 | NM_001100812.2 | c.*15C>T | 3_prime_UTR_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCL16 | ENST00000293778.12 | c.*15C>T | 3_prime_UTR_variant | 5/6 | 1 | NM_001386809.1 | P1 | ||
CXCL16 | ENST00000574412.6 | c.*15C>T | 3_prime_UTR_variant | 5/5 | 1 | P1 | |||
CXCL16 | ENST00000576153.5 | c.*15C>T | 3_prime_UTR_variant | 3/4 | 2 | ||||
CXCL16 | ENST00000575168.1 | n.611C>T | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.280 AC: 42498AN: 152010Hom.: 7353 Cov.: 32
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GnomAD3 exomes AF: 0.352 AC: 88372AN: 251412Hom.: 16721 AF XY: 0.351 AC XY: 47711AN XY: 135884
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GnomAD4 exome AF: 0.343 AC: 494138AN: 1442246Hom.: 87877 Cov.: 28 AF XY: 0.344 AC XY: 247018AN XY: 718708
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GnomAD4 genome ? AF: 0.279 AC: 42506AN: 152128Hom.: 7356 Cov.: 32 AF XY: 0.285 AC XY: 21180AN XY: 74352
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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