1-1013855-G-A
Position:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005101.4(ISG15):c.4-129G>A 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 1,297,970 control chromosomes in the GnomAD database, including 585,724 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.89 ( 61792 hom., cov: 33)
Exomes 𝑓: 0.96 ( 523932 hom. )
Consequence
ISG15
NM_005101.4 intron
NM_005101.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.255
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 1-1013855-G-A is Benign according to our data. Variant chr1-1013855-G-A is described in ClinVar as [Benign]. Clinvar id is 1185395.Status of the report is criteria_provided_single_submitter, 1 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 | c.4-129G>A | intron_variant | ENST00000649529.1 | NP_005092.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ISG15 | ENST00000649529.1 | c.4-129G>A | intron_variant | NM_005101.4 | ENSP00000496832 | P1 | ||||
ISG15 | ENST00000624652.1 | c.-21-129G>A | intron_variant | 3 | ENSP00000485313 | |||||
ISG15 | ENST00000624697.4 | c.-21-129G>A | intron_variant | 3 | ENSP00000485643 |
Frequencies
GnomAD3 genomes AF: 0.895 AC: 136143AN: 152102Hom.: 61776 Cov.: 33
GnomAD3 genomes
AF:
AC:
136143
AN:
152102
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.955 AC: 1094615AN: 1145750Hom.: 523932 AF XY: 0.955 AC XY: 542931AN XY: 568218
GnomAD4 exome
AF:
AC:
1094615
AN:
1145750
Hom.:
AF XY:
AC XY:
542931
AN XY:
568218
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.895 AC: 136202AN: 152220Hom.: 61792 Cov.: 33 AF XY: 0.897 AC XY: 66741AN XY: 74428
GnomAD4 genome
AF:
AC:
136202
AN:
152220
Hom.:
Cov.:
33
AF XY:
AC XY:
66741
AN XY:
74428
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3366
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
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
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at