rs11073795

Variant names:

• chr15-88637547-A-C
• rs11073795
• NM_001303233.2:c.-24-1796A>C

Your query was ambiguous. Multiple possible variants found:

• chr15-88637547-A-C
• chr15-88637547-A-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001303233.2(ISG20):​c.-24-1796A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: ISG20 NM_001303233.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ISG20	NM_001303233.2	c.-24-1796A>C		intron_variant	Intron 1 of 3		NP_001290162.1
ISG20	NM_001303234.2	c.-25+1255A>C		intron_variant	Intron 2 of 4		NP_001290163.1
ISG20	NM_001303235.2	c.-1681+1847A>C		intron_variant	Intron 1 of 2		NP_001290164.1
ISG20	NR_130134.2	n.69+1847A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ISG20	ENST00000379224.10	c.-142+1255A>C		intron_variant	Intron 2 of 5	3		ENSP00000368526.6
ISG20	ENST00000560741.5	c.-25+1255A>C		intron_variant	Intron 1 of 3	5		ENSP00000453638.1
ISG20	ENST00000558992.1	n.*119A>C		downstream_gene_variant		3

Frequencies

GnomAD3 genomes Cov.: 30

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.38

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

Other links and lift over

dbSNP: rs11073795; hg19: chr15-89180778;