1-1013490-C-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000624697.4(ISG15):c.-21-494C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.948 in 1,447,158 control chromosomes in the GnomAD database, including 652,127 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.90 ( 62121 hom., cov: 34)
Exomes 𝑓: 0.95 ( 590006 hom. )
Consequence
ISG15
ENST00000624697.4 intron
ENST00000624697.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.01
Genes affected
ISG15 (HGNC:4053): (ISG15 ubiquitin like modifier) The protein encoded by this gene is a ubiquitin-like protein that is conjugated to intracellular target proteins upon activation by interferon-alpha and interferon-beta. Several functions have been ascribed to the encoded protein, including chemotactic activity towards neutrophils, direction of ligated target proteins to intermediate filaments, cell-to-cell signaling, and antiviral activity during viral infections. While conjugates of this protein have been found to be noncovalently attached to intermediate filaments, this protein is sometimes secreted. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
Variant 1-1013490-C-G is Benign according to our data. Variant chr1-1013490-C-G is described in ClinVar as [Benign]. Clinvar id is 1185393.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ISG15 | NM_005101.4 | upstream_gene_variant | ENST00000649529.1 | NP_005092.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ISG15 | ENST00000624652.1 | c.-21-494C>G | intron_variant | 3 | ENSP00000485313 | |||||
ISG15 | ENST00000624697.4 | c.-21-494C>G | intron_variant | 3 | ENSP00000485643 | |||||
ISG15 | ENST00000649529.1 | upstream_gene_variant | NM_005101.4 | ENSP00000496832 | P1 |
Frequencies
GnomAD3 genomes AF: 0.898 AC: 136585AN: 152022Hom.: 62105 Cov.: 34
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GnomAD4 exome AF: 0.954 AC: 1234934AN: 1295018Hom.: 590006 Cov.: 19 AF XY: 0.954 AC XY: 623299AN XY: 653320
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GnomAD4 genome AF: 0.898 AC: 136643AN: 152140Hom.: 62121 Cov.: 34 AF XY: 0.900 AC XY: 66951AN XY: 74384
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 14, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 91% of patients studied by a panel of primary immunodeficiencies. Number of patients: 87. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Mendelian susceptibility to mycobacterial diseases due to complete ISG15 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational scores
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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