1-1013490-C-G

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.01
Variant links:
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
ISG15NM_005101.4 linkuse as main transcript upstream_gene_variant ENST00000649529.1 NP_005092.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ISG15ENST00000624652.1 linkuse as main transcriptc.-21-494C>G intron_variant 3 ENSP00000485313
ISG15ENST00000624697.4 linkuse as main transcriptc.-21-494C>G intron_variant 3 ENSP00000485643
ISG15ENST00000649529.1 linkuse as main transcript upstream_gene_variant NM_005101.4 ENSP00000496832 P1

Frequencies

GnomAD3 genomes
AF:
0.898
AC:
136585
AN:
152022
Hom.:
62105
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.742
Gnomad AMI
AF:
0.981
Gnomad AMR
AF:
0.936
Gnomad ASJ
AF:
0.910
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
0.968
Gnomad FIN
AF:
0.976
Gnomad MID
AF:
0.886
Gnomad NFE
AF:
0.959
Gnomad OTH
AF:
0.907
GnomAD4 exome
AF:
0.954
AC:
1234934
AN:
1295018
Hom.:
590006
Cov.:
19
AF XY:
0.954
AC XY:
623299
AN XY:
653320
show subpopulations
Gnomad4 AFR exome
AF:
0.721
Gnomad4 AMR exome
AF:
0.954
Gnomad4 ASJ exome
AF:
0.903
Gnomad4 EAS exome
AF:
1.00
Gnomad4 SAS exome
AF:
0.960
Gnomad4 FIN exome
AF:
0.970
Gnomad4 NFE exome
AF:
0.961
Gnomad4 OTH exome
AF:
0.937
GnomAD4 genome
AF:
0.898
AC:
136643
AN:
152140
Hom.:
62121
Cov.:
34
AF XY:
0.900
AC XY:
66951
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.741
Gnomad4 AMR
AF:
0.936
Gnomad4 ASJ
AF:
0.910
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
0.968
Gnomad4 FIN
AF:
0.976
Gnomad4 NFE
AF:
0.959
Gnomad4 OTH
AF:
0.908
Alfa
AF:
0.926
Hom.:
3709
Bravo
AF:
0.888
Asia WGS
AF:
0.967
AC:
3364
AN:
3478

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 submitterclinical testingUnidad de Genómica Garrahan, Hospital de Pediatría GarrahanNov 14, 2023This 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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Mendelian susceptibility to mycobacterial diseases due to complete ISG15 deficiency Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 14, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.53
DANN
Benign
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4615788; hg19: chr1-948870; API