NM_024066.3:c.931+12847T>C

Variant names:

• chr1-44235092-A-G
• rs4660781
• NM_024066.3:c.931+12847T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_024066.3(ERI3):​c.931+12847T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0334 in 152,302 control chromosomes in the GnomAD database, including 111 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 0.033 (111 hom., cov: 31)
• Consequence: ERI3 NM_024066.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 1 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]

ERI3-IT1 (HGNC:41431): (ERI3 intronic transcript 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0334 (5093/152302) while in subpopulation SAS AF = 0.0435 (210/4826). AF 95% confidence interval is 0.0395. There are 111 homozygotes in GnomAd4. There are 2528 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 111 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERI3	NM_024066.3	c.931+12847T>C		intron_variant	Intron 8 of 8	ENST00000372257.7	NP_076971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERI3	ENST00000372257.7	c.931+12847T>C		intron_variant	Intron 8 of 8	1	NM_024066.3	ENSP00000361331.2

Frequencies

GnomAD3 genomes AF: 0.0335 AC: 5095 AN: 152184 Hom.: 111 Cov.: 31

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0257

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0437

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0408

Gnomad OTH AF: 0.0355

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

GnomAD4 genome AF: 0.0334 AC: 5093 AN: 152302 Hom.: 111 Cov.: 31 AF XY: 0.0339 AC XY: 2528 AN XY: 74480

African (AFR) AF: 0.0170 AC: 707 AN: 41572

American (AMR) AF: 0.0257 AC: 393 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0571 AC: 198 AN: 3468

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.0435 AC: 210 AN: 4826

European-Finnish (FIN) AF: 0.0578 AC: 614 AN: 10614

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0408 AC: 2775 AN: 68022

Other (OTH) AF: 0.0351 AC: 74 AN: 2108

Alfa AF: 0.0406 Hom.: 83

Bravo AF: 0.0305

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.83
PhyloP100		0.098
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: rs4660781; hg19: chr1-44700764;