15-88637547-A-G

Variant names:

• chr15-88637547-A-G
• rs11073795
• ENST00000890265.1:c.-1820A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001303233.2(ISG20):​c.-24-1796A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,058 control chromosomes in the GnomAD database, including 23,600 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 0.55 (23570 hom., cov: 30)
  • Exomes 𝑓: 0.60 (30 hom.)
• Consequence: ISG20 NM_001303233.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001303233.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ISG20	NM_001303233.2		c.-24-1796A>G		intron	N/A	NP_001290162.1
	ISG20	NM_001303234.2		c.-25+1255A>G		intron	N/A	NP_001290163.1
	ISG20	NM_001303235.2		c.-1681+1847A>G		intron	N/A	NP_001290164.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ISG20	ENST00000890265.1		c.-1820A>G		5_prime_UTR	Exon 1 of 3	ENSP00000560324.1
	ISG20	ENST00000890264.1		c.-1820A>G		5_prime_UTR	Exon 1 of 2	ENSP00000560323.1
	ISG20	ENST00000379224.10	TSL:3	c.-142+1255A>G		intron	N/A	ENSP00000368526.6

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83840 AN: 151778 Hom.: 23546 Cov.: 30

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.562

GnomAD4 exome AF: 0.599 AC: 97 AN: 162 Hom.: 30 AF XY: 0.597 AC XY: 74 AN XY: 124

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 1.00 AC: 4 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 0.600 AC: 6 AN: 10

European-Finnish (FIN) AF: 0.625 AC: 10 AN: 16

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.620 AC: 67 AN: 108

Other (OTH) AF: 0.444 AC: 8 AN: 18

GnomAD4 genome AF: 0.552 AC: 83896 AN: 151896 Hom.: 23570 Cov.: 30 AF XY: 0.552 AC XY: 40938 AN XY: 74230

African (AFR) AF: 0.446 AC: 18460 AN: 41400

American (AMR) AF: 0.601 AC: 9180 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1976 AN: 3470

East Asian (EAS) AF: 0.606 AC: 3115 AN: 5142

South Asian (SAS) AF: 0.587 AC: 2826 AN: 4816

European-Finnish (FIN) AF: 0.536 AC: 5644 AN: 10524

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40875 AN: 67966

Other (OTH) AF: 0.560 AC: 1179 AN: 2106

Alfa AF: 0.587 Hom.: 76412

Bravo AF: 0.552

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.31
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11073795; hg19: chr15-89180778;