rs17155227

Variant names:

• chr8-9104480-C-T
• rs17155227
• ENST00000518663.2:c.298-11868C>T

Variant summary

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

The ENST00000518663.2(ERI1):​c.298-11868C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,184 control chromosomes in the GnomAD database, including 1,276 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 0.12 (1276 hom., cov: 32)
• Consequence: ERI1 ENST00000518663.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639
• Publications: 3 publications found

Genes affected

ERI1 (HGNC:23994): (exoribonuclease 1) Enables 3'-5' exonuclease activity. Predicted to be involved in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Located in cytoplasm and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ERI1 Gene-Disease associations (from GenCC):

• Hoxha-Aliu syndrome

  Inheritance: AR Classification: MODERATE Submitted by: G2P
• spondyloepimetaphyseal dysplasia, Guo-Campeau type

  Inheritance: AR Classification: MODERATE Submitted by: G2P

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERI1	ENST00000518663.2	c.298-11868C>T		intron_variant	Intron 3 of 3	5		ENSP00000518573.1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18640 AN: 152066 Hom.: 1277 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0936

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0828

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.122 AC: 18630 AN: 152184 Hom.: 1276 Cov.: 32 AF XY: 0.118 AC XY: 8807 AN XY: 74402

African (AFR) AF: 0.126 AC: 5215 AN: 41490

American (AMR) AF: 0.0933 AC: 1425 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.0831 AC: 401 AN: 4828

European-Finnish (FIN) AF: 0.0793 AC: 841 AN: 10608

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9691 AN: 68014

Other (OTH) AF: 0.130 AC: 274 AN: 2110

Alfa AF: 0.131 Hom.: 555

Bravo AF: 0.123

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.76
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs17155227; hg19: chr8-8961990;