rs6601288

Positions:

• chr8-9085920-A-T

Variant summary

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

The NM_001354638.2(ERI1):​c.808-2540A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 151,944 control chromosomes in the GnomAD database, including 35,795 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 0.67 (35795 hom., cov: 31)
• Consequence: ERI1 NM_001354638.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERI1	NM_001354638.2	c.808-2540A>T		intron_variant
ERI1	XM_047422402.1	c.808-2540A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERI1	ENST00000518663.2	c.300-30428A>T		intron_variant		5
ERI1	ENST00000520332.6	c.400-2540A>T		intron_variant		3
ERI1	ENST00000522612.2	c.53-2540A>T		intron_variant, NMD_transcript_variant		3
ERI1	ENST00000522258.1	n.150-13939A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101620 AN: 151826 Hom.: 35776 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.0790

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.669 AC: 101667 AN: 151944 Hom.: 35795 Cov.: 31 AF XY: 0.654 AC XY: 48538 AN XY: 74230

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.0792

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.658

Alfa AF: 0.704 Hom.: 4720

Bravo AF: 0.666

Asia WGS AF: 0.324 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6601288; hg19: chr8-8943430;