rs17155181

Variant names:

• chr8-9080675-T-C
• rs17155181
• NM_001354638.2:c.808-7785T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001354638.2(ERI1):​c.808-7785T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,200 control chromosomes in the GnomAD database, including 1,719 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 (1719 hom., cov: 32)
• Consequence: ERI1 NM_001354638.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERI1	NM_001354638.2	c.808-7785T>C		intron_variant	Intron 6 of 7		NP_001341567.1
ERI1	XM_047422402.1	c.808-7785T>C		intron_variant	Intron 6 of 7		XP_047278358.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERI1	ENST00000520332.6	c.400-7785T>C		intron_variant	Intron 4 of 5	3		ENSP00000518572.1
ERI1	ENST00000518663.2	c.298-35673T>C		intron_variant	Intron 3 of 3	5		ENSP00000518573.1
ERI1	ENST00000522258.1	n.149+17891T>C		intron_variant	Intron 2 of 2	3
ERI1	ENST00000522612.2	n.52-7785T>C		intron_variant	Intron 1 of 3	3		ENSP00000518574.1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21629 AN: 152082 Hom.: 1715 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.142 AC: 21631 AN: 152200 Hom.: 1719 Cov.: 32 AF XY: 0.137 AC XY: 10177 AN XY: 74408

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0847

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.154

Alfa AF: 0.156 Hom.: 242

Bravo AF: 0.141

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17155181; hg19: chr8-8938185;