chr8-9080312-T-G

Variant names:

• chr8-9080312-T-G
• rs17155179
• NM_001354638.2:c.808-8148T>G

Variant summary

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

The NM_001354638.2(ERI1):​c.808-8148T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,238 control chromosomes in the GnomAD database, including 1,707 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 0.14 (1707 hom., cov: 32)
• Consequence: ERI1 NM_001354638.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.749
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001354638.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERI1	NM_001354638.2		c.808-8148T>G		intron	N/A	NP_001341567.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERI1	ENST00000520332.6	TSL:3	c.400-8148T>G		intron	N/A	ENSP00000518572.1
	ERI1	ENST00000518663.2	TSL:5	c.298-36036T>G		intron	N/A	ENSP00000518573.1
	ERI1	ENST00000522258.1	TSL:3	n.149+17528T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21527 AN: 152122 Hom.: 1705 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0850

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.141 AC: 21530 AN: 152238 Hom.: 1707 Cov.: 32 AF XY: 0.136 AC XY: 10142 AN XY: 74428

African (AFR) AF: 0.130 AC: 5394 AN: 41546

American (AMR) AF: 0.114 AC: 1740 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3472

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

South Asian (SAS) AF: 0.107 AC: 515 AN: 4824

European-Finnish (FIN) AF: 0.0850 AC: 902 AN: 10612

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

European-Non Finnish (NFE) AF: 0.170 AC: 11587 AN: 67992

Other (OTH) AF: 0.154 AC: 325 AN: 2116

Alfa AF: 0.0836 Hom.: 106

Bravo AF: 0.140

Asia WGS AF: 0.0660 AC: 228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.57
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs17155179; hg19: chr8-8937822;