8-9032588-C-T

Position:

• chr8-9032588-C-T

Variant summary

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

The NM_153332.4(ERI1):​c.*2554C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,002 control chromosomes in the GnomAD database, including 13,740 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 0.39 (13740 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ERI1 NM_153332.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERI1	NM_153332.4	c.*2554C>T		3_prime_UTR_variant	7/7	ENST00000250263.8	NP_699163.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERI1	ENST00000250263.8	c.*2554C>T		3_prime_UTR_variant	7/7	1	NM_153332.4	ENSP00000250263	P1

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59486 AN: 151884 Hom.: 13715 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.413

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.392 AC: 59530 AN: 152002 Hom.: 13740 Cov.: 32 AF XY: 0.404 AC XY: 30014 AN XY: 74300

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.420

Alfa AF: 0.433 Hom.: 7448

Bravo AF: 0.387

Asia WGS AF: 0.592 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.74

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

Publications

LitVar

Other links and lift over

dbSNP: rs1045529; hg19: chr8-8890098;