chr1-44308055-G-A

Variant names:

• chr1-44308055-G-A
• rs325143
• NM_024066.3:c.758+255C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024066.3(ERI3):​c.758+255C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,946 control chromosomes in the GnomAD database, including 26,355 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 0.57 (26355 hom., cov: 32)
• Consequence: ERI3 NM_024066.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 7 publications found

Genes affected

ERI3 (HGNC:17276): (ERI1 exoribonuclease family member 3) Enables RNA binding 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). [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERI3	NM_024066.3	c.758+255C>T		intron_variant	Intron 6 of 8	ENST00000372257.7	NP_076971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERI3	ENST00000372257.7	c.758+255C>T		intron_variant	Intron 6 of 8	1	NM_024066.3	ENSP00000361331.2

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86328 AN: 151828 Hom.: 26349 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.568 AC: 86352 AN: 151946 Hom.: 26355 Cov.: 32 AF XY: 0.567 AC XY: 42138 AN XY: 74254

African (AFR) AF: 0.325 AC: 13471 AN: 41396

American (AMR) AF: 0.627 AC: 9583 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2270 AN: 3466

East Asian (EAS) AF: 0.736 AC: 3806 AN: 5168

South Asian (SAS) AF: 0.688 AC: 3305 AN: 4802

European-Finnish (FIN) AF: 0.597 AC: 6286 AN: 10530

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45708 AN: 67978

Other (OTH) AF: 0.587 AC: 1240 AN: 2112

Alfa AF: 0.597 Hom.: 4209

Bravo AF: 0.558

Asia WGS AF: 0.678 AC: 2356 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	3.2
DANN	Benign	0.46
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs325143; hg19: chr1-44773727; COSMIC: COSV64830753; COSMIC: COSV64830753;