1-1013855-G-A

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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.255
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 -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
ISG15NM_005101.4 linkuse as main transcriptc.4-129G>A intron_variant ENST00000649529.1 NP_005092.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ISG15ENST00000649529.1 linkuse as main transcriptc.4-129G>A intron_variant NM_005101.4 ENSP00000496832 P1
ISG15ENST00000624652.1 linkuse as main transcriptc.-21-129G>A intron_variant 3 ENSP00000485313
ISG15ENST00000624697.4 linkuse as main transcriptc.-21-129G>A intron_variant 3 ENSP00000485643

Frequencies

GnomAD3 genomes
AF:
0.895
AC:
136143
AN:
152102
Hom.:
61776
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.731
Gnomad AMI
AF:
0.980
Gnomad AMR
AF:
0.933
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:
0.906
GnomAD4 exome
AF:
0.955
AC:
1094615
AN:
1145750
Hom.:
523932
AF XY:
0.955
AC XY:
542931
AN XY:
568218
show subpopulations
Gnomad4 AFR exome
AF:
0.715
Gnomad4 AMR exome
AF:
0.951
Gnomad4 ASJ exome
AF:
0.904
Gnomad4 EAS exome
AF:
1.00
Gnomad4 SAS exome
AF:
0.961
Gnomad4 FIN exome
AF:
0.969
Gnomad4 NFE exome
AF:
0.962
Gnomad4 OTH exome
AF:
0.939
GnomAD4 genome
AF:
0.895
AC:
136202
AN:
152220
Hom.:
61792
Cov.:
33
AF XY:
0.897
AC XY:
66741
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.730
Gnomad4 AMR
AF:
0.933
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:
0.907
Alfa
AF:
0.921
Hom.:
8139
Bravo
AF:
0.884
Asia WGS
AF:
0.968
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 submitterclinical testingGenome-Nilou LabJul 14, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
2.0
DANN
Benign
0.50

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs2465124; hg19: chr1-949235; API