8-9080312-T-G

Position:

• chr8-9080312-T-G

Variant summary

Our verdict is Benign. Variant got -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

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/exons	MANE	UniProt
ERI1	NM_001354638.2	c.808-8148T>G		intron_variant
ERI1	XM_047422402.1	c.808-8148T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERI1	ENST00000518663.2	c.300-36036T>G		intron_variant		5
ERI1	ENST00000520332.6	c.400-8148T>G		intron_variant		3
ERI1	ENST00000522612.2	c.53-8148T>G		intron_variant, NMD_transcript_variant		3
ERI1	ENST00000522258.1	n.149+17528T>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0850

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.154

Alfa AF: 0.0815 Hom.: 101

Bravo AF: 0.140

Asia WGS AF: 0.0660 AC: 228 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	3.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17155179; hg19: chr8-8937822;