rs6601286

chr8-9082525-C-Achr8-9082525-C-G

Variant summary

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

The NM_001354638.2(ERI1):c.808-5935C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,146 control chromosomes in the GnomAD database, including 1,654 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 (1654 hom., cov: 32)
• Consequence: ERI1 NM_001354638.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

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=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERI1	NM_001354638.2	c.808-5935C>A		intron_variant
ERI1	XM_047422402.1	c.808-5935C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERI1	ENST00000518663.2	c.300-33823C>A		intron_variant		5
ERI1	ENST00000520332.6	c.400-5935C>A		intron_variant		3
ERI1	ENST00000522612.2	c.53-5935C>A		intron_variant, NMD_transcript_variant		3
ERI1	ENST00000522258.1	n.150-17334C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21257 AN: 152028 Hom.: 1651 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.000960

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.140 AC: 21258 AN: 152146 Hom.: 1654 Cov.: 32 AF XY: 0.135 AC XY: 10023 AN XY: 74384

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.152

Alfa AF: 0.0805 Hom.: 99

Bravo AF: 0.138

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	11
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6601286; hg19: chr8-8940035;