chr17-4739388-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001386809.1(CXCL16):c.-49G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00262 in 1,611,992 control chromosomes in the GnomAD database, including 69 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.012 ( 37 hom., cov: 31)
Exomes 𝑓: 0.0016 ( 32 hom. )
Consequence
CXCL16
NM_001386809.1 5_prime_UTR
NM_001386809.1 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.287
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
?
Variant 17-4739388-C-T is Benign according to our data. Variant chr17-4739388-C-T is described in ClinVar as [Benign]. Clinvar id is 777097.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0121 (1842/152354) while in subpopulation AFR AF= 0.0396 (1647/41588). AF 95% confidence interval is 0.038. There are 37 homozygotes in gnomad4. There are 858 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 36 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCL16 | NM_001386809.1 | c.-49G>A | 5_prime_UTR_variant | 1/6 | ENST00000293778.12 | ||
CXCL16 | NM_001100812.2 | c.-49G>A | 5_prime_UTR_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCL16 | ENST00000293778.12 | c.-49G>A | 5_prime_UTR_variant | 1/6 | 1 | NM_001386809.1 | P1 | ||
CXCL16 | ENST00000574412.6 | c.-49G>A | 5_prime_UTR_variant | 1/5 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0120 AC: 1834AN: 152236Hom.: 36 Cov.: 31
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GnomAD3 exomes AF: 0.00330 AC: 815AN: 246778Hom.: 8 AF XY: 0.00248 AC XY: 333AN XY: 134264
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GnomAD4 exome AF: 0.00163 AC: 2386AN: 1459638Hom.: 32 Cov.: 32 AF XY: 0.00144 AC XY: 1046AN XY: 726162
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GnomAD4 genome ? AF: 0.0121 AC: 1842AN: 152354Hom.: 37 Cov.: 31 AF XY: 0.0115 AC XY: 858AN XY: 74494
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at