rs8038865
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001303233.2(ISG20):c.-24-1472G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,020 control chromosomes in the GnomAD database, including 9,509 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.32 ( 9509 hom., cov: 32)
Consequence
ISG20
NM_001303233.2 intron
NM_001303233.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.39
Genes affected
ISG20 (HGNC:6130): (interferon stimulated exonuclease gene 20) Enables 3'-5' exonuclease activity and RNA binding activity. Involved in defense response to virus; negative regulation of viral genome replication; and nucleobase-containing compound catabolic process. Located in cytoplasm and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ISG20 | NM_001303233.2 | c.-24-1472G>C | intron_variant | ||||
ISG20 | NM_001303234.2 | c.-24-1472G>C | intron_variant | ||||
ISG20 | NM_001303235.2 | c.-1681+2171G>C | intron_variant | ||||
ISG20 | NR_130134.2 | n.69+2171G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ISG20 | ENST00000379224.10 | c.-141-1089G>C | intron_variant | 3 | P1 | ||||
ISG20 | ENST00000560741.5 | c.-24-1472G>C | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.325 AC: 49325AN: 151902Hom.: 9495 Cov.: 32
GnomAD3 genomes
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151902
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.325 AC: 49380AN: 152020Hom.: 9509 Cov.: 32 AF XY: 0.320 AC XY: 23750AN XY: 74320
GnomAD4 genome
?
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AC:
49380
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152020
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32
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23750
AN XY:
74320
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Asia WGS
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579
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at