8-9104480-C-T

Position:

• chr8-9104480-C-T

Variant summary

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

The ENST00000518663.2(ERI1):​c.300-11868C>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

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=-0.84).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERI1	ENST00000518663.2	c.300-11868C>T		intron_variant		5

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

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0933

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0831

Gnomad4 FIN AF: 0.0793

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.130

Alfa AF: 0.136 Hom.: 320

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17155227; hg19: chr8-8961990;